how to add formal charges on chemdoodle

Answer ChemDoodle Sketcher Questions

Some OWLv2 questions require you use the ChemDoodle Sketcher tool to draw a model of a molecule.

ChemDoodle Sketcher lets you draw the structural formula of a molecule by adding atoms, bonds, and rings to your model using the buttons at the top.

A question might begin with the ChemDoodle Sketcher displaying a single atom, an undefined dot, or a model that is nearly complete for you to finish.

Click Submit Answer .

Instructions:

Draw a complete structure for a molecule with the molecular formula CH 4 S.

Explicitly draw all H atoms.
In cases where there is more than one answer, just draw one.

the ChemDoodle Sketcher tool displaying one carbon atom.

Open the dropdown menu next to the element button, and select S .

Open the Set Label dropdown menu and select H .

angelaclasneutirud1988's Ownd

Chemdoodle help formal charge

2022.11.14 19:59 Praey for the gods ps5
2022.11.14 08:17 Google web designer banners

1000 / 1000

Attention! Your ePaper is waiting for publication!

By publishing your document, the content will be optimally indexed by Google via AI and sorted into the right category for over 500 million ePaper readers on YUMPU.

This will ensure high visibility and many readers!

Your ePaper is now published and live on YUMPU!

You can find your publication here:

Share your interactive ePaper on all platforms and on your website with our embed function

ChemDoodle v5.0 User Guide

chemdoodle.com

You also want an ePaper? Increase the reach of your titles

YUMPU automatically turns print PDFs into web optimized ePapers that Google loves.

The Future of Scientific Software

ChemDoodle

®

v5.0

User Guide

electronic, mechanical, photocopying, recording, or otherwise, without the prior written permission of iChemLabs.

ChemDoodle and MolGrabber are trademarks of iChemLabs, LLC.

All other trademarks are the property of their respective holders.

Content

Introduction

About ChemDoodle ............................ 10

About this Guide ................................. 10

Additional Information ....................... 10

Installation and System Requirements 11

Microsoft Windows Requirements .. 11

Macintosh OS X Requirements ....... 11

Linux Requirements ......................... 11

Installing Java ...................................... 11

Installation ........................................... 11

Installing for Multiple Users on a Single

Computer ............................................. 11

Windows .......................................... 12

Mac OS X ........................................ 12

Linux ................................................ 12

Folder Contents ................................... 12

Standard Operating System Documents

Folder .................................................. 13

Free Trials ........................................... 13

Trial Restrictions ................................. 13

Unrestricted Trials ............................... 13

Student Version Restrictions ............... 13

Activation ............................................ 14

Connection Issues ............................... 14

Firewall Issues ................................. 14

Proxy Issues ..................................... 14

Usage Restrictions .............................. 14

Attributions ......................................... 14

Chapter 1: Introducing

Overview ............................................. 15

The ChemDoodle Graphical User

Interface ............................................... 15

Using the Graphical User Interface ..... 17

Doodle Board ...................................... 17

Ruler Guides .................................... 18

Scrollbars ......................................... 18

Tab Tray ........................................... 18

1

Documents .......................................... 19

Creating a Document ....................... 19

Opening a Document ....................... 20

File Chooser Previews ..................... 20

Changing Document Size ................. 21

Discard Recent Changes to a

Document ......................................... 21

Saving Documents ........................... 22

Autosaving ........................................ 22

Reversing Actions ............................ 22

Mouse Cursors ................................. 22

Selected Content .............................. 23

The Workspace .................................... 24

Resizing the Workspace ................... 24

Resetting to the Default Workspace . 24

Reverting to the Last Saved

Workspace ........................................ 24

Saving the Current Workspace ......... 24

Menus .................................................. 25

ChemDoodle Menu (Mac OS X Only)

.......................................................... 25

File Menu ......................................... 25

Edit Menu ......................................... 27

View Menu ....................................... 28

Content Menu ................................... 29

Structure Menu ................................. 32

Reaction Menu ................................. 37

Spectrum Menu ................................ 37

Window Menu .................................. 37

Purchase Menu ................................. 38

Help Menu ........................................ 38

Toolbars ............................................... 39

Group Buttons .................................. 39

Files + Formatting Toolbar ............... 40

Content Toolbar ................................ 40

Strokes Toolbar ................................ 41

Labels Toolbar .................................. 41

Rings Toolbar ................................... 41

Bonds Toolbar .................................. 42

Arrows Toolbar ................................ 43

Orbitals Toolbar ............................... 43

Shapes Toolbar ................................. 43

Interface Options ................................. 45

Drawing Controls ............................. 45

Drawing Mode ................................. 45

Optimize Zone Size .......................... 45

Hover Distance ................................. 45

Snap to Grid ..................................... 45

Single Bond Behavior ...................... 45

Label Behavior ................................. 45

Auto-connect Rings and Templates . 45

Fix Bond Lengths ............................. 45

Fix Bond Angles .............................. 45

Require Starting Atom ...................... 45

Rotate Atom Text with Structures .... 46

Bonds are Focusable ........................ 46

3D Rotation Mode ............................ 46

Appearance ....................................... 46

Recently Opened Files ..................... 46

Interface Font ................................... 46

Interface Color ................................. 46

Decorations ...................................... 46

Show Unfixed Drawing

Measurements .................................. 46

Show Transform Measurements ...... 46

View Crawling Ants Effect When

Lassoing ............................................ 46

View Shimmer Effect on Button

Hover ................................................ 46

View Mouse Position on Rules ........ 46

View Selection Bounds on Rulers .... 46

Filechooser Settings ......................... 46

Unified Filechooser Memory ........... 46

Include Previews in Filechooser ...... 46

Chapter 2: Widgets

Overview ............................................. 47

Widget Windows ................................. 47

Widget Expansion ............................... 47

Widget List .......................................... 48

Widget Dock ....................................... 48

Widget Icons ....................................... 49

Elemental Analysis Widget ................. 50

Purpose ............................................. 50

Interface ............................................ 50

History Widget .................................... 50

2

Line Notation Pad Widget ................... 51

Purpose ............................................. 51

Interface ............................................ 51

MolGrabber Widget ............................ 52

Purpose ............................................. 52

Interface ............................................ 52

Directing to the Online Database ..... 54

Database Notes ................................. 54

Multiplet Tool Widget ......................... 56

Purpose ............................................. 56

Interface ............................................ 56

Simulating Multiplets ....................... 57

Setting up the Multiplet Figure ........ 57

Editing Multiplets from the Doodle

Board ................................................ 57

Memory and Runtime Issues ........... 58

NMR SignalSeek Widget .................... 58

Purpose ............................................. 58

Interface ............................................ 58

Simulating NMR .............................. 59

Analyzing the Results ...................... 59

How NMR is Simulated ................... 60

Properties Widget ................................ 60

Purpose ............................................. 60

Interface ............................................ 61

Search Widget ..................................... 62

Purpose ............................................. 62

Interface ............................................ 62

Search Settings ................................. 63

Statistics Widget ................................. 64

Purpose ............................................. 64

Interface ............................................ 64

Symbols Widget .................................. 65

Purpose ............................................. 65

Interface ............................................ 65

Templates Widget ................................ 67

Purpose ............................................. 67

Interface ............................................ 67

Using Templates ............................... 67

TLC Canvas Widget ............................ 68

Purpose ............................................. 68

Interface ............................................ 68

Drawing TLC Plates ......................... 69

Editing TLC Plates from the Doodle

Board ................................................ 70

Chapter 3: Basic Structures

Overview ............................................. 71

KeyBoard Shortcuts ............................ 71

Atoms .................................................. 71

Placing Carbon Atoms ..................... 71

Placing Other Elements .................... 71

Placing Atoms with Non-elemental

Labels ............................................... 72

Hovering Atoms ............................... 72

Selecting Atoms ............................... 72

Changing Atom Labels to other

Elements ........................................... 72

Changing Atom Labels to Nonelemental

Text .................................. 73

Repeating the last Typed Atom Label

for other Atoms ................................ 73

Moving an Atom .............................. 73

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

Chemical Labels .................................. 73

Atom Label Tool .............................. 73

Atom Label Token Stacking ............. 74

Formatting Atom Labels .................. 74

Atom Label Orientation ................... 75

Bonds .................................................. 75

Placing a Single Bond ...................... 75

Placing Bonds other than Single

Bonds ............................................... 76

Optimize Zone .................................. 76

Placing Bonds with Fixed Lengths

and Angles ........................................ 76

Placing Bonds at Non-fixed Lengths

.......................................................... 76

Placing Bonds at Non-fixed Angles . 76

and Non-fixed Angles ...................... 76

Hovering Bonds ............................... 76

Selecting Bonds ............................... 77

Changing a Bond Type ..................... 77

3

Changing Selected Bonds to Single

Bonds ............................................... 77

Incrementing a Bond Order .............. 77

Deleting a Bond ............................... 77

Deleting Bonds Around Atoms ........ 77

Changing the Z-Order of Bonds ...... 77

Chains ................................................. 78

Placing Chains at Fixed Angles ....... 78

Placing Chains at Non-fixed Angles 79

Forcing the Placement of Chains

Vertically and Horizontally .............. 79

Inverting Carbon Chains .................. 79

Rings ................................................... 79

Placing a Ring .................................. 79

Optimize Zone .................................. 79

Placing Rings with Fixed Lengths and

Angles .............................................. 80

Placing Rings at Non-fixed Lengths 80

Placing Rings at Non-fixed Angles .. 80

Placing Rings at Non-fixed Lengths

and Non-fixed Angles ...................... 80

Adding Rings to Bonds .................... 80

Templates ............................................ 80

Selecting a Template for Use ........... 81

Placing a Template ........................... 81

Optimize Zone .................................. 81

Placing Templates with Fixed Lengths

and Angles ........................................ 81

Placing Templates at Non-fixed

Lengths ............................................. 82

Angles .............................................. 82

Lengths and Non-fixed Angles ........ 82

Saving a New Template .................... 82

Managing your Templates ................ 82

Attributes ............................................. 82

Adding Attributes ............................. 83

Hovering Attributes .......................... 83

Selecting Attributes .......................... 83

Editing Attributes ............................. 83

Moving Attributes ............................ 84

Removing Attributes ........................ 84

Charges ................................................ 84

Adding Charges ................................ 84

Incrementing and Decrementing

Charges ............................................. 84

Removing Charges ........................... 84

Radicals ............................................... 85

Adding Radicals ............................... 85

Incrementing and Decrementing the

Number of Radical Electrons ........... 85

Removing Radicals .......................... 85

Symbols ............................................... 85

Adding Symbols ............................... 86

Removing Symbols .......................... 86

Isotopes ............................................... 86

Setting Published Isotope Mass

Numbers ........................................... 86

Setting Arbitrary Isotope Mass

Removing Mass Numbers ................ 86

Orbitals ................................................ 86

Placing Orbitals at Fixed Lengths and

Angles .............................................. 87

Placing Orbitals at Non-fixed lengths

or Angles .......................................... 88

Forcing Orbitals to be Drawn

Vertically and Horizontally .............. 88

Moving Orbitals ............................... 88

Resizing Orbitals .............................. 88

Removing Orbitals ........................... 88

Chapter 4: Shapes

Overview ............................................. 89

Anchors ............................................... 89

Control Anchors ............................... 89

Corner/Edge Anchors ....................... 89

Lines .................................................... 89

Drawing Lines at Fixed Angles ........ 89

Drawing Lines at Non-fixed Angles 90

Forcing the Lines to be Drawn

Vertically and Horizontally .............. 90

Moving Lines ................................... 90

Resizing Lines .................................. 90

Removing Lines ............................... 90

4

Arcs ..................................................... 90

Drawing Arcs at Fixed Angles ......... 91

Drawing Arcs at Non-fixed Angles .. 91

Forcing the Arcs to be Drawn

Vertically and Horizontally .............. 91

Moving Arcs ..................................... 91

Resizing Arcs ................................... 91

Changing Arc Angles ....................... 92

Flipping an Arc’s Orientation ........... 92

Removing Arcs ................................. 92

Arrows ................................................. 92

Drawing Arrows at Fixed Angles ..... 92

Drawing Arrows at Non-fixed Angles

.......................................................... 93

Vertically and Horizontally .............. 93

Moving Arrows ................................ 93

Resizing Arrows ............................... 93

Changing Arrow Arc Angles ............ 93

Removing Arrows ............................ 94

Editing Arrowheads ......................... 94

Rectangles ........................................... 94

Drawing Rectangles ......................... 94

Drawing Squares .............................. 95

Moving Rectangles .......................... 95

Resizing Rectangles ......................... 95

Converting Between Rounded and

Non-rounded Rectangles .................. 95

Removing Rectangles ...................... 95

Ovals ................................................... 95

Drawing Ovals ................................. 96

Drawing Circles ............................... 96

Moving Ovals ................................... 96

Resizing Ovals ................................. 96

Removing Ovals ............................... 96

Brackets ............................................... 96

Drawing Brackets ............................. 97

Drawing Brackets with Equal Width

and Height ........................................ 97

Moving Brackets .............................. 97

Resizing Brackets ............................. 97

Editing Bracket Lip Protrusion ........ 97

Removing Brackets .......................... 98

Custom Shapes .................................... 98

Drawing with the Pen Tool ............... 98

Drawing with the Polyline Tool ....... 99

Moving Pen Paths and Polylines ...... 99

Modifying Pen Paths and Polylines . 99

Drawing with the Bezier Tool .......... 99

Modifying Bezier Curves ............... 100

Deleting Bezier Control Points ...... 100

Adding Arrows to Bezier Curves ... 100

Closing and Opening Custom Shapes

........................................................ 100

Removing Custom Shapes ............. 101

Rulers ................................................ 101

Drawing Rulers at Fixed Angles .... 101

Drawing Rulers at Non-fixed Angles

........................................................ 101

Forcing Rulers to be Drawn Vertically

and Horizontally ............................ 101

Automatically Measuring Object

Width and Height ........................... 101

Diagonal ......................................... 102

Moving Rulers ............................... 102

Resizing Rulers .............................. 102

Showing and Hiding Major and Minor

Ticks ............................................... 102

Changing the Measurement Unit ... 102

Removing Rulers ........................... 103

Text Areas ......................................... 103

Chapter 5: Editing Content

Overview ........................................... 104

Selecting Content .............................. 104

Selecting Individual Objects .......... 104

Selecting Groups of Objects .......... 104

Select All ........................................ 105

Adding/Removing Individual Objects

from a Selection ............................. 105

Adding/Removing Groups of Objects

Selecting Whole Molecules ........... 105

Selecting Chemical Objects by

SMARTS ........................................ 105

5

Navigating Through Single Shapes 105

Selecting Only Shapes ................... 105

Select the Inverse of the Current

Selection ......................................... 106

Deselecting Objects ....................... 106

Reselecting Objects ........................ 106

Duplicating Content .......................... 106

Copy and Paste ............................... 106

Cut and Paste .................................. 106

Organizing Content ........................... 106

Aligning .......................................... 106

Aligning by Bond ........................... 106

Centering ........................................ 107

Distributing ..................................... 107

Flipping .......................................... 107

Flipping a Bond .............................. 107

Stacking .......................................... 108

Framing Content ............................... 108

Editing Content ................................. 108

Translating ...................................... 108

Translating Horizontally or Vertically

........................................................ 108

Duplicating Content ....................... 108

Rotating .......................................... 108

Moving the Rotation Anchor .......... 109

Scaling ............................................ 109

Fonts ............................................... 110

Drawing Aids .................................... 110

Atom Aids ...................................... 110

Bond Aids ....................................... 110

Ring Aids ....................................... 110

Molecule Aids ................................ 110

Background Aids ............................ 110

Colors ................................................ 110

Color Button ................................... 110

Quick Colors Button ...................... 111

Color Detection .............................. 111

Color Chooser ................................ 111

Modifying the Z-order of Shapes ...... 112

Grouping Content ............................. 112

Grouping ......................................... 113

Ungrouping ..................................... 113

Removing Content ............................ 113

Removing individual Objects ........ 113

Removing Groups of Objects ......... 113

Chapter 6: Advanced Chemistry and

Cheminformatics

Aromaticity ....................................... 114

Toggling between Kekulé and Circle

Representations for Aromatics ....... 114

Forcing Aromaticity ....................... 114

Calculating Covalent Bonds ............. 114

Carbon Labels ................................... 115

Terminal Carbon Labels ................. 115

Chemical Suppliers ........................... 115

Chemical Warnings ........................... 116

Warning Types ............................... 116

Disabling Warnings Globally ......... 116

Disabling Warnings for a Single Atom

........................................................ 116

Hiding Warnings from Rendering .. 117

Cleaning Structures ........................... 117

Optimizing Structures in 2D .......... 117

Distance Geometry Embedding ...... 117

Preserving Stereochemistry ........... 117

Descriptors ........................................ 117

Constitutional ................................. 117

Topological ..................................... 118

Physicochemical ............................. 119

ADME ............................................ 120

Flattening Atomic Coordinates ...... 120

Fragmentation ................................... 120

Formal Charges ................................. 121

Glassware Clipart .............................. 121

Flipping Glassware ......................... 122

Tubing ............................................. 122

Graph Reduction ............................... 123

Reduce 0° (Lone) ........................... 123

Reduce 1° (Terminals) ................... 123

Repeatedly Reduce 1° .................... 123

Reduce 1° + 0° ............................... 123

Reduce 2° (Chains) ........................ 123

Reduce 2° + 1° + 0° ....................... 123

Hydrogens ......................................... 123

Implicit Hydrogen Rendering ......... 123

6

Adding Hydrogens as Atoms ......... 124

Adding Hydrogens as Text ............. 124

Defining when Hydrogens are Added

to Carbons ...................................... 124

IUPAC Naming ................................. 124

Name to Structure .......................... 124

Kekulé Structures .............................. 124

Kekulizing a Single Bond Frame ... 124

Kekulizing a Substructure of

Resonance Bonds ........................... 125

Label Expansion ................................ 125

Expanding Labels ........................... 125

Implicit Hydrogens ........................ 125

Condensed Labels .......................... 125

Abbreviations ................................. 126

Adding Custom Abbreviations ....... 126

Mixing Condensed Notations and

Molecular Formulas ....................... 126

Newman Projections ......................... 127

Ring Perception ................................. 127

Supported Ring Sets ....................... 127

Exploding Ring Sets ...................... 128

Performance Considerations .......... 128

Sequence Tool ................................... 128

Stereochemistry ................................ 128

Chiral Centers ................................ 129

Double Bonds ................................. 129

Resolving Stereochemistry ............ 129

Forcing Stereochemical

Configurations ................................ 129

Structure Perspective ......................... 129

Unique IDs ........................................ 130

Zero Order/Ionic Bonds .................... 130

Chapter 7: Reactions

Overview ........................................... 131

Drawing Reaction Arrows ................. 131

Arrow Types ...................................... 131

Arrowhead Styles ........................... 131

Changing Arrowhead Lengths and

Angles ............................................ 131

Quickly Toggle Arrowheads .......... 131

Connector Styles ............................ 132

Special Arrow Presets .................... 132

Bezier Arrow Ideas ........................... 132

The Chute Arrow ............................ 133

The Loop Arrow ............................. 133

The Escalator Arrow ...................... 133

The Hump Arrow ........................... 133

The Zigzag Arrow .......................... 133

Building Reactions ............................ 133

Implicitly ........................................ 133

Explicitly ........................................ 133

Adding Reaction Conditions .......... 134

Adding Plus Symbols ..................... 134

Dissolving Reactions ........................ 134

Cleaning Reactions ........................... 134

Chapter 8: Spectra

Overview ........................................... 137

Inserting Spectra ................................ 137

Spectra Types ................................. 137

Uninterpretable Spectra .................. 138

Saving Spectra ................................... 138

Simulating Spectra ............................ 138

Editing Spectra .................................. 138

Moving Spectra .............................. 138

Resizing Spectra ............................. 139

Removing Spectra .......................... 139

Expanding the Perspective ............. 139

Editing the Perspective ................... 139

Changing the Title .......................... 140

Changing the Axes ......................... 140

Showing Grids ............................... 140

Showing Integration Lines ............. 140

Chapter 9: Visual Specifications

Overview ........................................... 142

Document Settings ............................ 142

Style Sheets .................................... 142

Setting the Default Document Settings

........................................................ 143

Restore the Original Default

Document Settings ......................... 143

Individual Settings ............................ 143

7

Setting Types .................................. 143

Page ................................................ 144

Atoms ............................................. 144

Attributes ........................................ 146

Bonds ............................................. 146

Rings .............................................. 147

Reactions ........................................ 148

Shapes ............................................ 148

Spectra ............................................ 149

Editing Visual Specifications ............ 149

For Single Objects .......................... 149

For a Group of Objects .................. 150

Conforming a Group of Objects to the

Current Style Sheet ........................ 150

Conforming the Entire Document to a

Different Style Sheet ...................... 150

3D Graphics ...................................... 150

Bond Stroke Styles ............................ 151

Advanced Document Rendering ....... 151

Anti-Aliasing .................................. 152

Font Fractional Metrics .................. 152

Dithering ......................................... 153

Rendering Algorithm ...................... 154

Alpha Interpolation Algorithm ....... 154

Color Rendering Algorithm ............ 154

Stroke Control ................................ 154

Image Scaling ................................. 156

Chapter 10: Sharing Information

Overview ........................................... 157

The System Clipboard ....................... 157

MIME Types .................................. 157

Clipboard Settings .......................... 158

Scalable Vector Graphics ............... 158

Copying Data to Other Applications 159

Using the Copy Function ............... 159

Using the Copy As Function .......... 159

Pasting Data from Other Applications

........................................................... 160

Where Content is Pasted ................ 160

Paste Special... ............................... 160

Pasting Text as Chemical Data ....... 160

Chemical Format Compatibility ....... 161

Image Format Compatibility ............. 161

Supported Input Formats ................ 161

Supported Output Formats ............. 161

Importing Chemical Content from

Images ............................................ 162

Exporting the Document to an Image

........................................................ 162

Exporting only Certain Objects to an

Image .............................................. 162

Image Output Options .................... 162

Inserting Images ................................ 163

Round Trip Editing ............................ 163

Support ........................................... 163

Windows ........................................ 164

Mac OS X ...................................... 164

Linux .............................................. 165

Printing .............................................. 167

Page Setup ..................................... 167

Flipping the Page Orientation ........ 168

Print Preview .................................. 168

Printing a Document ...................... 168

Appendix A: Managing

Overview ........................................... 169

Application and File Icons ................ 169

Updating ChemDoodle ...................... 169

Windows Administrator Privileges 170

Skipping Updates ........................... 170

Purchasing Upgrades ..................... 170

Moving your Activated Copy to a New

Computer ........................................... 170

Preparing for a System Restore ......... 171

Using iChemLabs Cloud Services .... 171

Appendix B: Chemical File Types

Overview ........................................... 172

Adherence to Third Party Specifications

........................................................... 172

Be Careful Saving 3rd Party Formats

Testing 3rd Party File Type Output ... 172

Supported Chemical File Types ........ 173

8

File Annotations ................................ 173

File Conversion Tool ......................... 174

iChemLabs ChemDoodle Documents

........................................................... 175

iChemLabs ChemDoodle Javascript

Data ................................................... 175

ACD/ChemSketch Document ........... 176

Beilstein ROSDAL ............................ 177

CambridgeSoft ChemDraw Files ...... 177

CHARMM CARD File ..................... 180

ChemAxon Marvin Documents ........ 180

Chemical Markup Language ............. 182

Daylight SMILES .............................. 183

IUPAC InChI ..................................... 184

IUPAC JCAMP Data ......................... 185

MDL ISIS Sketch Files ..................... 186

MDL Connection Table Files ............ 190

Molinspiration JME String ................ 192

RCSB Protein Data Bank Files ......... 193

Schrödinger Files .............................. 194

Standard Molecular Data ................... 195

About ............................................. 195

Tripos Mol2 ....................................... 196

Tripos Sybyl Line Notation ............... 197

XYZ .................................................. 197

Appendix C: Compatibility with 3rd

Party Applications

Overview ........................................... 199

Microsoft Office ................................ 199

Word ............................................... 199

Powerpoint ..................................... 199

Excel ............................................... 199

Apple iWork ...................................... 199

Pages .............................................. 199

Keynote .......................................... 199

Numbers ......................................... 199

OpenOffice ........................................ 199

Writer ............................................. 199

Calc ................................................ 200

Impress ........................................... 200

Adobe Products ................................. 200

Photoshop ...................................... 200

Illustrator ........................................ 200

Browsers ........................................... 200

Other .................................................. 200

Appendix D: Elemental Data

Overview ........................................... 201

Elemental Database ........................... 201

References ......................................... 201

Interactive Periodic Table .................. 201

Appendix E: How NMR is

Simulated

Algorithms ........................................ 204

Shift Prediction .............................. 204

Splitting .......................................... 204

Roof Effects ................................... 204

Solvent Peaks ................................. 204

1H Rapid Exchange ........................ 204

1H Anisotropic Effects ................... 204

1H Diastereotopic Pairs ................. 204

13C Quaternary Carbon Intensity

Reductions ...................................... 204

Limitations ........................................ 204

Appendix F: ChemDoodle Web

Components

Overview ........................................... 206

Generating ChemDoodle Web

Components ...................................... 206

Generating Javascript Data Files for Use

with ChemDoodle Web Components 207

Optimizing PDB Files ....................... 207

Generating Components for Mobile

Devices .............................................. 208

Rendering Compatibility .................. 208

License .............................................. 208

Am I allowed to use this? .................. 209

Attributions ....................................... 209

Further Information ........................... 209

Appendix G: ChemDoodle Mobile

Overview ........................................... 210

9

Supported Platforms .......................... 210

iOS .................................................. 210

Android .......................................... 210

Logging in to ChemDoodle Mobile .. 210

ChemDoodle Mobile Features .......... 210

Calculations .................................... 210

Spectra ............................................ 210

Transferring Data between ChemDoodle

Desktop and ChemDoodle Mobile .... 211

Appendix ICL-1: Technical Support

When to Contact Customer Service .. 212

How to Contact Customer Service .... 212

Feature Requests ............................... 213

Following ChemDoodle Development

........................................................... 214

Troubleshooting ................................. 214

Windows ........................................ 214

Mac OS X ...................................... 214

Performance Improvements ........... 214

This User Guide provides information on the

iChemLabs product, ChemDoodle.

About ChemDoodle

ChemDoodle, in short, can create images of

molecules. But it is much more than that.

ChemDoodle can efficiently generate

chemical documents and figures for use in

publications, produces non-molecular objects

such as spectra and TLC plates, is integrated

with databases, can manipulate a large

number of chemical files and formats, and in

general, streamlines a lot of the tasks that one

is confronted with when trying to do or

explain chemistry in a digital medium.

ChemDoodle isn't just another program for

drawing molecules, it's a brand new

application for interacting with chemical data

and creating chemical art!

ChemDoodle is designed to be intuitive and

easy to learn. ChemDoodle is used by a wide

range of individuals, from high school

students to accomplished professors and we

have done our best to provide the most

intuitive controls for such a diverse group

while remaining thorough and providing

superior quality.

ChemDoodle is integrated with the following

iChemLabs Products:

• ChemDoodle Web Components

• ChemDoodle Mobile

About this Guide

This User Guide contains information for the

ChemDoodle application for the Windows,

Mac OS X and Linux operating systems. It

10

assumes you are familiar with the basics of

your operating system. If you are not, please

refer to your system manual before using

ChemDoodle.

Some tasks described in this guide require the

use of third-party applications such as

Microsoft Office Word or iWork Pages. If you

are not familiar with these third-party

applications, please consult the associated

user guide provided with that product.

The chapters in this guide are organized by

task. They are intended to help you

familiarize yourself with the ChemDoodle

application and to begin using it as quickly

and efficiently as possible.

Most images are taken from the Mac OS X

version of ChemDoodle and will be

representative of all operating systems. If an

operating system specific issue is discussed,

any images are taken from the operating

system under investigation.

Additional Information

Additional sources of ChemDoodle

information include:

• ChemDoodle Support Pages.

http://www.chemdoodle.com/support

• ChemDoodle Videos.

http://www.chemdoodle.com/videos

• ChemDoodle Web Components.

http://web.chemdoodle.com

• ChemDoodle Mobile.

http://mobile.chemdoodle.com

• iChemLabs Customer Support.

http://www.ichemlabs.com/contact-us

• iChemLabs Website.

http://www.ichemlabs.com

Installation and System

Requirements

Microsoft Windows Requirements

• Windows XP, Vista or 7+.

• Oracle Java 1.6 or more recent.

• A minimum of 1GB of memory.

Macintosh OS X Requirements

• Mac OS X 10.6 (Snow Leopard) or 10.7

(Lion) or 10.8 (Mountain Lion).

• Oracle Java 1.6 or more recent (installed by

default on 10.6; for 10.7+, will be

automatically installed when ChemDoodle

is opened and you accept to install Java).

Linux Requirements

• Any version of Linux, although we test with

and Ubuntu (recommended), Mint, Fedora,

Debian and OpenSUSE Linux.

• Any GUI, although we recommend and test

with GNOME.

• Oracle Java 1.6 or more recent (OpenJDK,

GNU Java, IcedTea or any non-official

distributions are not supported).

Installing Java

ChemDoodle requires the official Oracle

(formerly Sun Microsystems) Java

distribution to run. Java is free and can be

easily installed from: http://www.java.com

Most contemporary Windows systems will

have Java installed by default.

Mac OS X 10.6 will have Java installed by

default. Mac OS X 10.7+ will prompt you to

install Java when you first run a Java

11

application. Accept that prompt to install

Java.

ChemDoodle does NOT support OpenJDK,

IcedTea, GNU Java, or any other non-Oracle

version of Java. With unsupported Java

distributions, ChemDoodle will run slowly,

have broken functions and may not even run

at all.

Installation

Installation, activation and uninstallation

instructions are can be found on the

ChemDoodle website.

Table 1: Websites for Installation Instructions

Operating

System

Webpage

Windows http://

www.chemdoodle.com/

windows-installationinstructions

Mac OS X http://

www.chemdoodle.com/osxinstallation-instructions

Linux http://

linux-installationinstructions

Installing for Multiple Users

on a Single Computer

ChemDoodle will allow several users to use

ChemDoodle on the same computer. All

preferences and settings files are saved

relative to the user’s account, so that each

user may save their own preferences. Note

that even though ChemDoodle only needs to

be installed once on the computer, each user

will still have to individually activate

ChemDoodle for his/her user account, so he/

she will need access to an activation code.

Instructions for installing ChemDoodle for

multiple users is operating system dependent

and is described in the following subsections.

Windows

During the installation, keep the install folder

in C:\Program Files\. All users will be able to

execute ChemDoodle from within this folder.

There will be periodic updates to

ChemDoodle. For Windows Vista and later,

ChemDoodle requires administrator

privileges to update, so you will need to

update ChemDoodle as administrator on the

computer if none of the users have

administrator privileges. This only needs to

be done once for the computer, and all users

will be using the update.

Mac OS X

During the installation, drag the ChemDoodle

folder to the /Applications folder as

instructed. All users will be able to execute

ChemDoodle from within this folder.

ChemDoodle. Only superusers will be able to

update ChemDoodle, so you will need to

update ChemDoodle as superuser on the

computer if none of the users are superusers.

This only needs to be done once for the

computer, and all users will be using the

update.

Linux

Run the Linux BIN in a folder that all users

have rights to execute binaries from. After the

installation, verify that all users that will be

using ChemDoodle have the necessary

permissions to do so.

ChemDoodle. You should restrict write

12

privileges to the ChemDoodle installation

folder if you do not want users to update

ChemDoodle by themselves. This may be

necessary, for instance, if you do not want

one user to update the application while

another user is finishing some work and does

not yet want to learn the changes the update

will bring. If you restrict write permissions,

you will need to update ChemDoodle as root

on the computer when all users are ready.

Folder Contents

There are two folders that the ChemDoodle

application uses, the main ChemDoodle

installation folder and the

ChemDoodleSettings folder located in the

operating system’s standard Documents

folder.

The contents of the main ChemDoodle

installation folder are:

1. ChemDoodle application -

ChemDoodle.exe on Windows,

ChemDoodle.app on Mac OS X, and the

ChemDoodle shell script on Linux

2. config directory - This folder contains

various configuration files, such as

proxy.config, for setting ChemDoodle to

use your proxy. It also contains the site

license configuration file for site licenses.

3. docs directory - This folder contains

documentation such as this user guide.

4. external directory - This folder contains

required packages that ChemDoodle

needs to start up and run properly. Any

licenses associated with these packages

are also provided.

5. resources directory - This folder contains

native application icon images and other

resources such as the auto-updater and the

ChemDoodle Web Components library.

6. ChemDoodle.jar - The executable java

jar of ChemDoodle. Do not remove this

file! This jar is not present in the Mac OS

X distribution of ChemDoodle.

7. ChemDoodle.vmoptions - This file is

only present in the Windows distribution

of ChemDoodle. It contains parameters

for the Java virtual machine.

WARNING: Do not remove or alter any of

the contents of the ChemDoodle installation

folder or unexpected behavior may occur.

To move the application, you must move

the entire ChemDoodle folder.

Standard Operating System

Documents Folder

The standard operating system Documents

folder varies depending on the operating

system:

• Windows XP - C:\Documents and Settings\

[username]\My Documents

• Windows Vista/7 - C:\Users\[username]

\My Documents

• Mac OS X - /Users/[username]/Documents

• Linux - /Users/[username]/Documents

Free Trials

Trials may be initiated by clicking the Free

Trial button on the activation screen when

ChemDoodle is opened. Trials will remain

active for 14 days. After a trial expires, there

is no option to try it again.

13

Trial Restrictions

• Documents show a watermark at the top

and will render a background texture.

• The Save..., Save as Image... and

Convert... functions are disabled.

• Only images and ChemDoodle data can be

pasted from ChemDoodle.

• All copied and printed content will contain

a watermark.

• Templates cannot be saved.

• Certain ChemDoodle Web Components

functions are disabled (such as PDB file

optimization).

Unrestricted Trials

If your trial has expired and you still require

the use of ChemDoodle, or if you would like

to try ChemDoodle without the trial

restrictions, you may purchase an unrestricted

14 day trial on the ChemDoodle website.

Student Version Restrictions

The student version of ChemDoodle has

several restrictions:

• No iChemLabs account is provided.

• Round-trip editing is not available.

• Images output from ChemDoodle will not

contain chemical metadata.

• Formatted documents and publishing style

sheets are not available.

• Import/Export of style sheets is disabled.

• Only ChemDoodle Documents can be

saved.

• No conversion utility.

• The only chemical data format you can

copy is the ChemDoodle format.

Activation

Activation is performed when one uses a

purchased activation code to associate a

license with the ChemDoodle application for

a given user account.

Activation can be performed in two ways.

The first is by using the activation code in the

activation screen when ChemDoodle has not

been activated or a trial started. The second

way is to use the Activate ChemDoodle

menu item in the Purchase menu while a trial

is active.

The activation code may be manually typed

into the activation form, but it is easier to just

copy and paste the entire code from the

receipt into the form. Once activated with a

purchased license, all restrictions from the

trial are removed.

Activation requires an active internet

connection. Our server is sent the activation

code which is validated and gives permission

to create the license file. This method

prevents piracy and allows us to minimize the

cost of ChemDoodle. There are no exceptions

to this activation procedure.

Connection Issues

Activation is an important part of the setup

procedure, and there are a few issues, usually

in corporate environments, that may occur.

Firewall Issues

If your firewall blocks internet connections

from Java applications, then ChemDoodle

will not be allowed to connect to the internet.

An administrator should set up a special

exception to allow ChemDoodle to connect to

the internet, at least for activation.

14

Proxy Issues

If you use a proxy to access the internet,

ChemDoodle will use the default system

proxy information to connect to the internet.

If that fails, then you will need to manually

define the proxy settings in the proxy.config

file that is located in the config folder in the

ChemDoodle installation folder.

Usage Restrictions

There are no restrictions on how to use

ChemDoodle as long as the user abides by the

license he/she accepts when activating

There are no restrictions on your created

chemical drawings generated from activated

copies of ChemDoodle. You may use your

created chemical drawings for whatever

purpose you choose.

Using ChemDoodle to output the glassware

graphics for the sole purpose of publishing,

selling, or distributing them individually or as

a set is forbidden.

Attributions

Attribution of graphics and output to

ChemDoodle are welcome, but are not

necessary in any form.

Toolbars

Chapter 1:

Introducing

Overview

This section introduces the new user to the

ChemDoodle graphical user interface. It

covers the following topics:

• Identifying the parts of the ChemDoodle

interface.

• Creating, opening and saving documents.

• Introducing the menus and toolbars.

Figure 1.1: ChemDoodle on Windows (7)

15

The ChemDoodle Graphical

User Interface

Although the Windows, Mac OS X and Linux

versions of the ChemDoodle graphical user

interface (GUI) differ slightly, the main

elements of the GUI are consistent across

platforms. The Windows version of

ChemDoodle is shown in Figure 1.1. The

Mac OS X version of ChemDoodle is shown

in Figure 1.2. The Linux version of

ChemDoodle is shown in Figure 1.3.

Menu Bar

Doodle Board

Widgets

Widget

Figure 1.2: ChemDoodle on Mac OS X (10.6)

Figure 1.3: ChemDoodle on Linux (Ubuntu 10.04)

16

Menu Bar Doodle Board

Dock

Using the Graphical User

Interface

ChemDoodle’s functions are accessed

through interaction with several types of

components:

Ruler Guides

• Doodle Board - The main drawing window.

• Menus - Core application functions.

• Toolbars - Quickly access functions and

modify how mouse gestures interact with

the Doodle Board.

• Widgets - Mini applications within

ChemDoodle that perform powerful and

complementary tasks.

Figure 1.4: The Doodle Board

Tab Tray

17

These components are identified in Figures

1.1-1.3 and are discussed in the following

sections. Widgets are explained in Chapter 2.

The Doodle Board is the main drawing

window and contains all of the documents

you create and edit. You may use mouse

gestures to interact with the Doodle Board

and to draw your figures. Figure 1.4 displays

the main components of the Doodle Board.

Selected Content

Document

Mouse Cursor

There are two rulers aligned with the

currently displayed document on the Doodle

Board. The ruler to the left of the document

allows for vertical measurements and the

ruler to the top of the document allows for

horizontal measurements.

When the document rendering scale is

changed, the ruler scale will also change to

match the new dimensions. When the

scrollbars are used to focus on a different area

of the document, the rulers will also scroll to

match the new location.

The ruler displays full ticks at each inch, halfticks

at each half-inch, and quarter-ticks every

eighth of an inch. Several colored ticks and

areas may also be present on the rules for

visual feedback. These feedback tips can be

disabled in the Preferences window under the

General tab.

• Margin Areas - Margins are highlighted in

a yellow color.

• Mouse Pointer Ticks - Mouse pointer

locations are ticked on the rules with a red

color.

• Selection Dimension Area - Marks the

bounds of the currently selected content.

This is denoted by an amber area. This area

corresponds to the internal coordinates of

the content and not the visual bounds. For

example, it will denote the bounding box

given the atom coordinates, but will ignore

the dimensions of the labels for those

atoms.

Scrollbars

Scrollbars will appear to the right and bottom

of the document if the height and width,

respectively, of the document are too large to

fit on the Doodle Board. You can click and

drag the scroll bars to change which area of

18

the document is displayed on the Doodle

Board. You can also use the mouse scroll

gesture to change the perspective. Horizontal

mouse scrolling is only supported on Mac OS

X.

The Doodle Board stores all drawing content

and organizes them into documents that can

be saved as files or images. Each document

has a corresponding tab, located at the bottom

of the Doodle Board in the tab tray. When a

tab is pressed, the corresponding document

will be selected and viewed. This allows you

to manage a large number of files at once,

without having to manage a large number of

windows.

The number of tabs present in the tab tray will

change depending on how many documents

are open. If only a single document is present,

then only one tab is displayed and will be

selected. Selected tabs are colored a light

blue, as is shown in Figure 1.5.

Figure 1.5: A single tab.

When multiple documents are open, multiple

tabs will be displayed in the tab tray. The tab

corresponding to the currently selected

document will be selected and displayed over

other tabs as is shown in Figure 1.6.

Figure 1.6: Multiple tabs.

If there are more tabs than can fit in the tab

tray, then only the most recently viewed tabs

that fit in the tab tray will be displayed. A

number and two right-oriented chevrons are

displayed to the right of the last tab to notify

you that some tabs are not displayed as is

shown in Figure 1.7.

Figure 1.7: There is 1 non-displayed tab.

Click on the chevrons and number to open a

popup menu that lists the undisplayed tabs as

is shown in Figure 1.8. Click on a choice to

select that document.

Figure 1.8: List non-displayed tabs.

There are also tab specific functions that can

be accessed by right-clicking on any given

tab:

• Close - Close the current tab. This option is

only enabled if multiple tabs are present.

• Close Others - Close the other tabs, but

leave the current one open. This option is

• New Document - Create a new document

and tab.

• Restore - If the corresponding document

was created by opening a file, then this

function will be enabled, allowing you to

undo all of your changes and reload the file.

The name of the file is displayed on the tab. If

the name is too long, it may be cropped and

appended with “...”. You may also see a '*'

and/or '^' displayed before a file name in a

tab. The '*' is a reminder that the file has been

changed since the last save, and the '^' marks

it as an online file.

Documents

The document represents a virtual sheet of

paper. Each document embodies one page of

the structures, objects and figures that you

19

create. The document is fully customizable

and also contains a definition of the styles of

the content within it. You can create new

blank documents, or read one from a file that

ChemDoodle recognizes.

Note: A visual specification is a definition

about how some object is rendered. For

example, a bond line width is a visual

specification for a bond. In this document,

such a concept may be referred to as a

visual specification, a style or a document

setting. They all mean the same thing.

Creating a Document

You can create a new, blank document using

the default ChemDoodle document settings,

or use a Chemical Document Settings file to

create a new formatted document.

To create a new blank document using the

default style sheet, select the New menu item

in the File menu.

To create a new blank document using a

predefined style sheet, select New Formatted

Document... in the File menu.

ChemDoodle provides built-in Chemical

Document Settings files. For example, the

ACS Document 1996 style is configured to

create documents that are set with the bond

lengths, bond width, spacing, and fonts used

in the 2-column format of all American

Chemical Society journals. Currently,

ChemDoodle provides the following style

sheets:

• ACS Document 1996

• Adv. Synth. Catal Document

• J. Chin. Chem. Soc. Document

• J. Het. Chem. Document

• J. Mol. Mod. Document (1 Column)

• J. Mol. Mod. Document (2 Column)

• Phytomedicine Document

• RSC Document (1 Column)

• RSC Document (2 Column)

• Science of Synthesis Document

• SYNTHESIS, SYNLETT Document

• Verlag Helv. Chim. Acta Document

• Wiley Document

These style sheets are presented when you

create a new formatted document as is shown

in Figure 1.9.

Figure 1.9: Creating a New Formatted Document.

The style sheets are organized into 3 sections.

The first contains just the default style sheet,

the second contains all the built-in style

sheets and the last contains custom style

sheets. Select the style sheet that you prefer,

and choose to set any custom dimensions, and

then click the Ok button to create your new

formatted document.

If you would like to modify the document

dimensions of the formatted document, then

select the Use Custom Dimensions checkbox

and edit the Page Size and Margins fields.

20

Opening a Document

To open a document, select the Open... menu

item from the File menu, locate the file you

would like to open with the file chooser that

appears and click the Open button.

ChemDoodle can read many file formats, and

the default file type the file chooser searches

for is a ChemDoodle Document. To allow

other file types, click on the format drop

down selection at the bottom of the file

chooser and select the file type you would

like to open, or select the All Files type.

NOTE: Selecting All Files will allow you to

select any file, including files that

ChemDoodle cannot read. If such a file is

chosen, you will see a file read error

displayed. Otherwise, ChemDoodle will try

to determine the type of file chosen by

analyzing the file extension and file content

to open it accordingly.

To open a recently opened document, enter

the Open Recent submenu in the File menu

and select the document you would like to

open. Only the 10 most recently opened files

are remembered.

File Chooser Previews

The file choosers that you use to open your

files will closely resemble the standard file

choosers that you use in all of your other

applications. However, we have added some

enhancements when using ChemDoodle. One

addition is chemical file type previews.

On all operating systems, you will see a

preview of chemical files that you select in

file choosers. On Windows, Mac OS X and

Linux, the file chooser will show a preview of

the entire document on the right as shown in

Figures 1.10, 1.11, and 1.12. On Windows

and Linux, these previews are interactive, if

you hover your mouse over the preview, that

area will zoom in for a closer inspection. On

Mac OS X, a tray is added to the bottom of

the file chooser to list the individual

molecules present in the file as shown in

Figure 1.12.

Figure 1.10: The file chooser on Windows

showing the file preview.

Figure 1.11: The file chooser on Linux showing

the file preview.

Figure 1.12: The file chooser on Mac OS X

showing the file preview and preview tray.

21

You can disable file chooser previews in the

Preferences window, under the General tab

in the Filechooser Settings section.

Changing Document Size

To change the size of the current document,

perform the following steps:

1. Choose the Resize Document... menu

item in the Edit menu.

2. Use the form to select a preset document

size or manually type in the desired

document dimensions.

3. Click the Ok button to resize the

document.

To retrieve the last saved version of a file

without using Undo functions, select the

Restore menu item in the File menu. All

changes made to the file since it was last

saved are discarded and the saved version of

the file will appear.

Saving Documents

To save your document as a file, select the

Save or Save As... menu items from the File

menu. Save will automatically save the

document to the file it is associated to, while

Save As... will allow you to save that file to a

new location or override other files. If there is

no file associated with a document, the Save

function will work identically to the Save

As... function.

After selecting a save function, a file chooser

will appear. Select the location you would

like to have the document saved in and type

in a name for the file if you do not like the

default name. You do not need to type in an

extension as ChemDoodle will do this for

you.

After you are satisfied with a location and

name, select the file type of the document to

be saved. By default, a ChemDoodle

Document is chosen, but you can choose

from a large selection of file types that

ChemDoodle can interpret.

NOTE: Only the ChemDoodle Document

can store your document with 100%

accuracy. Other file types are for other

purposes and may not define the same

objects and properties in ChemDoodle.

Keep this in mind while saving files. If you

forget, a small warning will popup when

saving to a file type other than a

ChemDoodle Document. These warnings

can be disabled in the Preferences window

under the Saving tab.

After selecting the file type to be used, press

the Save button to save your document as a

file.

Autosaving

ChemDoodle will automatically save unsaved

content for you at regular intervals. If your

computer shuts off unexpectedly, the next

22

time ChemDoodle opens, all autosaved

content will be displayed.

You can turn off autosaving in the

Preferences window under the Saving tab.

You can also specify the autosave interval in

the same section. The default autosave

interval is 5 minutes.

Reversing Actions

ChemDoodle keeps track of the actions you

perform. You can reverse actions one at a

time by selecting the Undo menu item in the

Edit menu then restore them with the Redo

menu item in the Edit menu. Once you close

your document, the undo queue is reset.

More advanced undo/redo functionality is

associated with the History widget.

Mouse Cursors

The mouse pointer is context sensitive and

will change when hovered over the document

to display visual feedback about the current

mouse gestures that can be performed. The

different mouse cursors are described in Table

3.

Table 3: Mouse Cursors

Cursor Means that...

Clicking and dragging perform

obvious functions.

This is the lasso cursor. Clicking

and dragging will generate an

outline following the drag path.

All content within the drag path

will be selected.

This pinpoints the exact location

that your click will hit. This

enhances accuracy when using

the rectangular marquee or when

placing shapes.

This signifies that a single object

may be selected.

This means that content can be

grabbed. Individual objects or

selected content can be grabbed.

This means that content has been

grabbed and dragging gestures

will perform appropriate actions.

This cursor only appears when

rotating structures in 3D. It

means that content can be

grabbed.

means that content has been

grabbed and drag gestures will

perform appropriate actions.

This cursor signifies that resize

actions can be performed by

clicking and dragging. This

cursor will also appear when

translating the rotation anchor.

This cursor signifies that rotation

clicking and dragging.

Content that is selected will be bordered by a

dashed amber line. Selected content can be

used in functions and sent to other

components. A crawling ants effect is on by

default to help the user keep track of selected

content. The crawling ants effect can be

23

For instructions on selecting content and

editing selected content, read Chapter 5.

The Workspace

The ChemDoodle workspace consists of the

application window and all interface elements

contained within. You may freely place

toolbars, select widgets, change the document

scale, select view options, etc., and the next

time you open ChemDoodle, your choices

will have been remembered. ChemDoodle

also provides several functions for managing

your workspace, so you have control over

how the application behaves.

Resizing the Workspace

A minimum screen resolution of 1280 by 800

pixels is recommended to neatly fit all of the

components in ChemDoodle on the screen.

Slightly smaller resolutions are still

acceptable when shrinking the document

scale. For much smaller resolutions, the

workspace will display scrollbars to access

the entire ChemDoodle interface.

On devices that just fit the ChemDoodle

window, ChemDoodle will expand to fit the

entire screen. On larger resolution devices,

ChemDoodle will open to take only as much

room as necessary. At any time, you may unexpand

the application or resize it to your

preference. Upon resizing, the widgets will be

replaced to the right of the workspace, and the

Doodle Board will be centered.

The workspace will keep track of the size and

location of ChemDoodle when it was last

closed.

Resetting to the Default Workspace

To reset to the default workspace that was

presented when ChemDoodle was first

opened, select the Default Workspace menu

item in the Window menu.

24

Workspace

To revert to the last saved workspace, select

the Revert Workspace menu item in the

Window menu.

Saving the Current Workspace

To save the current workspace, which will

override the revert workspace, perform the

following steps:

1. Organize the workspace to your

preference.

2. In the Window menu, select the Save

Workspace menu item.

The current workspace is now saved and can

be reverted to.

Note: ChemDoodle will automatically save

your current workspace upon close, so

make sure to revert the workspace to your

saved workspace before you close, if

necessary. Otherwise, ChemDoodle will

open up to look exactly like it was when it

was closed.

Menus

Menus are located on the top of the

ChemDoodle application. On Mac OS X, the

ChemDoodle menu bar is displayed in the

screen menu bar, as would be expected of

Mac OS X applications.

For menu item keyboard shortcuts, consult

the KeyboardShortcuts.pdf document in the

docs folder in the ChemDoodle installation

There are 9 menus in the menu bar (10 on

Mac OS X), not including the Purchase

menu that is present during the free trial:

• ChemDoodle - This is a Mac OS X specific

menu bar and contains access to several

Mac OS X specific tasks as well as the

About, Preferences and Quit menu items.

• File - This menu handles all input and

output of data, as well as file specific

functions such as Annotations.... You also

have access to your iChemLabs account

through this menu and the Quit menu item

is located here on non-Mac OS X platforms.

• Edit - Standard global document functions

are located here including Cut, Copy and

Paste.

• View - Functions for changing how

documents are shown are located here as

well as access to the elemental and

chemical data provided with ChemDoodle.

The dynamic periodic table is also

accessible through this menu.

• Content - Contains all non-chemical

functions for editing content in the current

• Structure - Contains all functions related to

editing and analyzing molecules.

25

• Reaction - Contains all functions related to

editing and analyzing reactions.

• Spectrum - Contains all functions related to

editing and analyzing spectra.

• Window - Manage your workspace and the

entire ChemDoodle application window.

• Purchase - This menu is only present

during the free trial and provides functions

for purchasing and activating licenses for

• Help - This menu contains several functions

to access this user guide, list references,

contact customer service and other common

help items.

• About ChemDoodle - Display information

about ChemDoodle, your activation code

and your license expiration, if any.

• Preferences... - Open the Preferences

window to edit ChemDoodle preferences.

• Services - Standard Mac OS X submenu

that will likely be empty.

• Hide ChemDoodle - Hide the ChemDoodle

application.

• Hide Others - Hide other applications.

• Show All - Show all hidden applications.

• Quit ChemDoodle - Quit the ChemDoodle

File Menu

• New - Add a new blank document to the

Doodle Board.

• New Formatted Document... - Add a new

blank formatted document to the Doodle

• Open - Open a recognized chemical file

that you locate with a file chooser.

• Open Recent> - The 10 most recently

opened chemical files are listed here. Click

a file to open it.

• Insert Image... - Add a recognized image

file to the current document that you locate

with a file chooser.

• Close - Close the current document. This

function is only enabled if two or more

documents are present.

• Close Others - Close all but the current

document. This function is only enabled if

two or more documents are present.

• Restore - Restores a file from its last save.

This function will only be enabled for files

that have been previously saved or were

opened from a preexisting file.

• Annotations... - Associate annotations with

the current document or view previously set

annotations.

• Save - Saves the current file with the

present save settings determined when

opening the file or by previously saving it.

This action will act exactly like the Save

As... function if the document is not yet

associated with a save location.

• Save As... - Save the current document as a

file type of your choice in a new file (or

override one) that you will locate with a file

chooser.

• Save As Image... - Save the current

document as an image that you will place

with a file chooser. Several bitmap and

vector image types are supported.

26

• Save Selection As Image... - Save the

currently selected objects as an image that

you will place with a file chooser. Several

bitmap and vector image types are

supported. This menu item is disabled if no

objects are selected.

• Convert... - Displays a window to convert

chemical files to different chemical file

types that ChemDoodle interprets. Nothing

is loaded to the Doodle Board, as output is

written directly to a new file that is created.

• Generate Web Component... - Generate a

ChemDoodle Web Component. An entire

window will appear for you to define and

edit the ChemDoodle Web Component, as

well as preview and generate the Javascript

for it. More information on this feature is

covered in Appendix F.

• Sync with Online Account... - Login to

your iChemLabs Account to access special

online features in ChemDoodle.

• Open Online File> - Your online files will

be listed in this submenu. Click on a file to

open it on the Doodle Board.

• Save As Online File... - Save your file

online. This is useful for using

ChemDoodle efficiently on several

computers or for interacting with

iChemLabs cloud services. This feature also

allows you to transfer structures drawn on

your desktop to ChemDoodle Mobile on

your phone.

• Refresh - Revalidate the menus and re-sync

your information with your online account.

This should be done when you transfer a

new file into your account from a source

other than ChemDoodle desktop.

• Logout - Logout from your iChemLabs

account.

• Page Setup... - Display the operating

system specific window for selecting initial

print settings.

• Print Preview - View the current document

in its entirety on the screen, ignoring

extraneous graphics such as errors and

visual aids.

• Print... - Print the current document.

• Exit - Exits ChemDoodle. This menu item

is in the ChemDoodle menu on Mac OS X,

listed as Quit ChemDoodle.

Edit Menu

• Undo - Undo the last action.

• Redo - Redo the last undone action.

• Cut - Copy the selected objects to the

system clipboard in addition to removing

them from the document.

• Copy - Copy the selected objects to the

system clipboard.

• Copy As> - Contains convenience functions

for quickly placing specific data on the

system clipboard as text and as a chemical

to be transferred to a range of 3rd party

applications that use that data type. This

submenu is only enabled if content is

selected.

• Daylight SMILES - Place a SMILES

string for the currently selected content

on the system clipboard as text and as a

chemical.

• IUPAC InChI - Place an InChI string

for the currently selected content on the

27

system clipboard as text and as a

• MDL MOLFile - Place a complete

molfile for the currently selected content

• Tripos SLN - Place a SLN string for the

currently selected content on the system

clipboard as text and as a chemical.

• Paste - Paste the system clipboard data of

highest priority into the document.

• Paste Text as Chemical> - Pastes the

current text on the clipboard, interpreted as

chemical data, as any of the options

provided in the submenu.

• IUPAC InChI - Paste text as InChI.

• Beilstein ROSDAL - Paste text as

ROSDAL.

• Daylight SMILES - Paste text as

SMILES.

• Tripos SLN - Paste text as SLN.

• XYZ-Like Data - Paste text as a

chemical, interpreted from a text blob

where XYZ-like data is parseable.

• Guess Chemical Format - Paste text as

chemical, where the format is guessed

from the content.

• Paste Special... - Lists all data that

ChemDoodle can interpret from the system

clipboard. You may then choose the data of

choice to be pasted into the document. This

function is useful, for instance, when you

would like to paste SMILES string text

instead of a structure into the document. A

structure has higher priority than text.

• Clear - Remove all content from the current

• Resize Document... - Resize the current

document. You may also change the page

margins in the Preferences window under

the Visuals tab under the Page tab.

• Conform Document... - Conform all

objects in the current document to a

selected style sheet. This function will also

change all fonts and scale all objects if you

choose to do so.

• Purge Clipboard - This function clears the

• Purge History - This function clears the

undo/redo history, which will reset the

History widget. This may be convenient if

the action list gets so long that it becomes

unmanageable and causes memory issues,

or if you would like to prevent yourself

from undoing past a certain action.

This menu item is in the ChemDoodle

menu on Mac OS X.

View Menu

• Hide Warnings - Hide all the warnings in

the document.

• Drawing Aids> - Display various guides to

help when drawing figures.

• Atoms> - Display guides associated to

• Show Circular Guidelines -

Display circular guides around

atoms with radii equal to the current

bond length document setting.

28

• Show Orthogonal Guidelines -

Display vertical and horizontal

guidelines that intersect through the

atom for aiding in alignment tasks.

• Bonds> - Display guides associated to

bonds.

• Show Parallel Guidelines - Display

a line that goes through the bond to

extrapolate where they point to.

• Rings> - Display guides associated to

rings.

• Color in Rings - Color in Euler

facet rings with a color code that

depends on the size of the ring.

• Molecules> - Display guides associated

to molecules.

• Show Molecule Bounds - Draw

rectangular bounding guides around

molecules to show their visual

bounds.

center of the molecule for aiding in

alignment tasks.

• Background> - Display guides

associated to the page.

• Show Crosshair - Displays a

crosshair.

• Show Grid Guidelines> - Displays

grids.

• Every Quarter-Inch - Displays

a grid with quarter-inch spacing.

• Every Half-Inch - Displays a

grid with half-inch spacing.

• Every Inch - Displays a grid

with inch spacing.

• Show Margin Guidelines -

Displays a rectangular region that

specifies the printable area of the

page.

• Unique IDs> - Associates ID attributes to

objects.

• On Atoms> - Associate IDs to atoms.

• Incremental - Associate

incremental IDs to atoms. The atoms

are numbered in chronological order

from when they were created.

• Morgan Indices - Associate

Morgan indices to atoms.

• On Bonds - Associate incremental IDs

to bonds. The bonds are numbered in

chronological order from when they

were created.

• Elemental Data - View the entire elemental

database packaged in ChemDoodle that is

used for all calculations and

cheminformatics functions. The data is

displayed in a dynamic table.

• Ionization Energies - View ionization

energies of the elements in a dynamic table.

This data is part of ChemDoodle’s

elemental database.

• Isotopes - View isotope data for the

elements in a dynamic table. This data is

part of ChemDoodle’s elemental database.

• Interactive Periodic Table - View an

interactive periodic table that can be

customized and printed. You may also use

its dynamic features to create nice

demonstrations.

29

• Actual Size - Negate any zoom effects.

• Current Selection - Center the current

selection on the Doodle Board. This

function is useful if the document

perspective is zoomed in and it is difficult

to locate selected content.

• Zoom Out - Zoom out and decrease the

document scale, you may also use the drop

down selection provided in the Files +

Formatting toolbar.

• Zoom In - Zoom in and increase the

Content Menu

• Select> - Contains various tools for

selecting content.

• All - Select all content in the current

• Inverse - Select all content in the

current document that isn’t currently

selected while deselecting all content in

the current document that is currently

• Next Molecule - Select the next

molecule in the document. This function

will traverse chronologically through

the molecules in the current document

based on the time they were drawn. If a

molecule isn’t currently selected, it will

first select the last molecule drawn.

• Next Shape - Select the next shape in

the document. This function will

traverse chronologically through the

shapes in the current document based on

the time they were drawn. If a shape

isn’t currently selected, it will first

select the last shape drawn.

• SMARTS... - A textfield will appear.

Type in the desired SMARTS pattern

here and then click the Accept button.

Any content in the current document

that matches the SMARTS pattern will

be selected.

• Deselect - Deselect all content that is

currently selected. This function is only

enabled if content is currently selected.

• Reselect - Reselect the last content that was

selected. This function is only enabled if no

content is currently selected. This function

may not work as expected when content is

removed. For instance, if you selected

content and then deleted it, then pressing

reselect will have no action because the

content to be reselected no longer exists.

• Center> - Contains various functions for

centering content.

• All on Page - Center all content on the

• Selection on Page - Center only the

currently selected content on the page.

• Selection Horizontally - Horizontally

center only the currently selected

content.

• Selection Vertically - Vertically center

only the currently selected content.

• Flip> - Contains functions for flipping

selected content.

• Horizontally - Flip the currently

selected content horizontally over its

midpoint.

• Vertically - Flip the currently selected

content vertically over its midpoint.

30

• Rotate> - Contains various functions for

rotating selected content.

• 90° CW - Rotate selected content

clockwise by 90 degrees.

• 90° CCW - Rotate selected content

counterclockwise by 90 degrees.

• 180° - Rotate selected content by 180

degrees.

• Arbitrary... - Rotate selected content by

an arbitrary angle that you input.

• Scale... - Scale the currently selected

objects. You will be presented with a

window to set various options to define how

the content will be scaled. You can even

choose to scale all molecules individually,

to set them all to a common bond length for

instance.

• Align Bond> - Contains functions for

aligning a single selected bond, rotating the

molecule it is contained in. This function is

enabled when only a single bond is selected.

• Up - Align bond up.

• Right - Align bond right.

• Down - Align bond down.

• Left - Align bond left.

• Flip Bond Orientation - Flip the

orientation of the bond. Non-symmetrical

bonds will face the other direction.

• Align> - Contains functions for aligning

• Left Edges - Align all selected content

by the left edges of their visual bounds.

• Horizontal Centers - Align all selected

content by the horizontal centers of their

visual bounds.

• Right Edges - Align all selected content

by the right edges of their visual

• Top Edges - Align all selected content

by the top edges of their visual bounds.

• Vertical Centers - Align all selected

content by the vertical centers of their

• Bottom Edges-Align all selected

content by the bottom edges of their

• Distribute> - Contains functions for

distributing selected content.

• Horizontally on Page - Distribute

selected content horizontally on the

page such that they are evenly

distributed based on their visual bounds

and fit within the page margins.

• Vertically on Page - Distribute selected

content vertically on the page such that

they are evenly distributed based on

their visual bounds and fit within the

page margins.

• Horizontally by Buffer Space... -

Distribute selected content horizontally

on the page such that they are evenly

by a value that you input.

• Vertically by Buffer Space... -

Distribute selected content vertically on

the page such that they are evenly

31

• Grid All on Page... - Grid all content on the

page. A window will appear to ask for row

and column information.

• Stack All on Page - Stack all content on the

page. Stacking will place all content within

the page margins based on their visual

bounds. Stacking proceeds by placing

content from left to right, and then top to

bottom, on the page using a small buffer

space.

• Group - Group the currently selected

content into a single shape. Single items in

grouped content can not be edited and

transformations will affect the entire group

as a whole. Groups can also be grouped into

larger groups.

• Ungroup - Ungroup grouped content.

Ungrouping is not recursive, so if the group

being ungrouped contains a group, then that

inner group will remain grouped.

• Join - If two atoms are selected, then they

will be joined into a single atom, and their

bonds will all point to the new joined atom.

If those atoms were part of two discrete

molecules, then one molecule is translated

to the other. If two bonds are selected, then

they will be joined together, and all bonds

connected to the joined bonds will connect

to the new joined bond. Two bonds within

the same molecule cannot be joined. One

molecule will be translated and rotated to

the other to aesthetically display the new

joined molecule. This function is disabled

in all other cases.

• Flatten - This function will change all zcoordinates

of selected atoms to be 0,

thereby flattening 3D structures.

• Add Frame> - Contains various functions

for surrounding selected content with

shapes based on their visual bounds.

• Square Brackets - Surround selected

content with square brackets based on

the content’s visual bounds.

• Parenthesis - Surround selected content

with parenthesis based on the content’s

• Curly Brackets - Surround selected

content with curly brackets based on the

content’s visual bounds.

• Chevrons - Surround selected content

with chevrons based on the content’s

• Rectangle - Surround selected content

with a rectangle based on the content’s

• Measure> - Contains various functions for

measuring selected content.

• Diagonal - Place one ruler object

diagonally over selected content based

on its visual bounds to measure its

diagonal. You can change the units of

the ruler object.

• Width and Height - Place two ruler

objects, one vertically to the left and one

horizontally below selected content

based on its visual bounds to measure

its width and height. You can change the

units of the ruler object.

• Conform to Document Settings - Conform

all currently selected objects to the current

chemical document settings, including

scaling and changing fonts.

32

Structure Menu

• Add/Remove Hydrogens> - Contains

functions for adding Hydrogens to

structures. Settings for defining how

Hydrogens will be added to structures can

be set in the Preferences window under the

Visuals tab under the Atoms tab.

• All - Add Hydrogens to all structures in

the current document.

• From Selection - Add Hydrogens only

to the currently selected structures.

• Add Attribute... - Add an attribute to the

selected object. This will only be enabled if

a single atom or bond is selected.

• Place Formal Charges - Will place formal

charges on atoms based on their valency.

• Calculate Covalent Bonds - This function

will deduce covalent bonds in structures

based on atomic 3D distances and the

covalent radii present in ChemDoodle’s

elemental database. This function is

dependent on the Ångström/Bond Length

document setting present in the Preferences

window under the Visuals tab. Only single

bond orders will be placed. This function is

very useful for working with files that may

not contain explicit topology, such as PDB

or XYZ files.

• Remove Selected Bonds - This function

will remove all selected bonds, leaving the

constituent atoms.

• Saturate - This function will change the

bond orders of all selected bonds to the

single bond order.

• Graph Reduction> - Contains several

functions for reducing the underlying graph

data structures that represent the selected

structures. This is ideal for extracting

information about small molecule building

blocks for drug discovery purposes.

• Reduce 0° (Lone) - This function will

remove all 0 degree nodes, so all lone

atoms will be removed.

• Reduce 1° (Terminals) - This function

will remove all 1 degree nodes, so all

terminal atoms will be removed.

• Repeatedly Reduce 1° - This function

will repeatedly remove all 1 degree

nodes until none remain, so all isolated

chains will be removed.

• Reduce 1° + 0° - This function will

remove all 0 and 1 degree nodes, so all

lone and terminal atoms will be

removed.

• Reduce 2° (Chains) - This function will

remove all 2 degree nodes, so all inner

chain atoms will be removed.

• Reduce 2° + 1° + 0° - This function will

remove all 0, 1 and 2 degree nodes, so

all lone, terminal and chain (including

non-isolated chains) atoms will be

• Expand Labels - Will expand all complex

atom labels to their all-atom equivalents.

• Rings> - Contains several functions for

defining ring sets in selected structures. If a

highly overlapping figure results, just stack

the content for a cleaner layout.

• Explode Smallest Set of Smallest

Rings - Explode out the smallest set of

smallest rings (SSSR) for selected

structures. The SSSR is the standard for

defining ring sets in flat 2D structures.

• Explode Euler Facet Rings - Explode

out the Euler facet rings for selected

33

structures. The Euler facet ring set is

better than the SSSR at defining

essential rings in 2D depictions of 3D

structures.

• Explode Hanser (All) Rings - Explode

every last graph cycle in selected

• Stereochemistry> - Contains several

functions for deducing the stereochemistry

of selected structures.

• Assign R/S (CIP) - Finds and assigns

CIP stereochemistry to chiral centers.

• Assign E/Z (CIP) - Finds and assigns

CIP stereochemistry to stereochemical

double bonds.

• Assign cis/trans - Finds and assigns cis/

trans stereochemistry to appropriate

• Chemical Suppliers> - Contains functions

to search for chemical suppliers for drawn

• Substructure Match - Find chemical

suppliers for the selected structure by

substructure search.

• Exact Match - Find chemical suppliers

for the selected structure by exact

match.

• Clean> - Contains various functions for

optimizing and beautifying selected

• 2D Optimization - The CCG depiction

algorithm is performed on your selected

structures to clean them in 2D.

• Distance Geometry Embedding -

Distance geometry is used on the bond

distance matrix of the selected

structures to embed them in 3D. This is

great for highly connected structures

like buckyballs and will produce

suitable 3D coordinates. It will not work

very well on less connected structures

like chains.

• Descriptors> - Contains various functions

that will display the named descriptor for

the first of the selected molecules. Details

about these algorithms are described in

Chapter 6.

• Last Chosen - This menu item is a

placeholder that will remember the last

chosen descriptor for easy repeat access.

• Constitutional> - Contains any

constitutional descriptors; descriptors

that are defined by the chemical makeup

of the molecule.

• Atom Count - Calculates the atom

count.

• Bond Count - Calculates the bond

• Degree of Unsaturation -

Calculates the degree of

unsaturation.

• Element Counts - Calculates the

element counts.

• Euler Facet Ring Count - Counts

the total number of Euler facet rings

present in a molecule.

• Exhaustive Ring Count - Counts

every last graph cycle in a molecule.

• Frèrejacque Number - Calculates

the Frèrejacque number. This is also

the SSSR number.

34

• Hydrogen Bond Acceptor Count -

Calculates the Hydrogen bond

acceptor count.

• Hydrogen Bond Donor Count -

Calculates the Hydrogen bond donor

• Rotatable Bond Count - Counts the

number of rotatable bonds.

• Total Electron Count - Counts the

total number of electrons present in

the molecule.

• Lightest Isotopic Mass - Calculates

the molecular mass based on the

lightest isotope for each element,

regardless of abundance.

• McGowans Characteristic Volume

- Calculates McGowan’s

characteristic volume.

• Molecular Mass - Calculates the

molecular mass based on

ChemDoodle’s elemental database.

• Volume as a Sum of Atomic and

Bond Contributions - Calculates

the ABC volume.

• Empirical Formula - Generates the

empirical formula of the first

selected structure.

• Molecular Formula - Generates the

molecular formula of the first

• Topological> - Contains any

topological descriptors; descriptors that

are defined by the bond connectivity of

• Centric Index - Calculates the

Centric index.

• Diameter - Calculates the longest

topological path in a molecule.

• Hosoya Index - Calculates the

Hosoya index.

• Molecular Topological Index -

Calculates the Molecular

Topological index.

• Platt Index - Calculates the Platt

index.

• Ring Complexity - Calculates the

Ring Complexity.

• Szeged Index - Calculates the

Szeged index.

• Wiener Index - Calculates the

Wiener index.

• Zagreb Indexes - Calculates

various Zegreb indexes.

• Balaban Index - Calculates the

Balaban index.

• Bertz Complexity Index -

Calculates the Bertz Complexity

• Branching Index - Calculates the

Branching index.

• Chi Molecular Connectivity

Indexes> - Calculates various Chi

Molecular Connectivity Indices.

• Fraction Molecular Framework -

Calculates the Fraction Molecular

Framework ratio.

35

• Harary Index - Calculates the

Harary index.

• Kappa Shape Indices> - Calculates

various Kappa Shape Indices.

• Superpendentic Index - Calculates

the Superpendentic index.

• Adjacency Matrix - Generates the

bond connectivity matrix.

• Bond Distance Matrix - Generates

the bond distance matrix.

• Bond Electron Matrix - Generates

the bond electron matrix.

• Detour Matrix - Generates the

detour matrix.

• Incidence Matrix - Generates the

incidence matrix.

• Laplacian Matrix - Generates the

Laplacian matrix.

• Physicochemical> - Contains any

physicochemical descriptors; descriptors

that are defined by physics or chemistry

• Average Molecular Polarizability>

- Calculates the average molecular

polarizability given several

algorithms.

• Critical Pressure - Calculates the

critical pressure of a molecule.

• Critical Temperature - Calculates

the critical temperature of a

molecule.

• Critical Volume - Calculates the

critical volume of a molecule.

• Enthalpy of Formation (ideal gas

at 298K) - Calculates the enthalpy

of formation of a molecule at the

stated conditions.

• Enthalpy of Fusion - Calculates the

enthalpy of fusion of a molecule.

• Enthalpy of Vaporization (at Tb) -

Calculates the enthalpy of

vaporization of a molecule at the

• Gibbs Energy of Formation (ideal

gas, unit fugacity, at 298K) -

Calculates the Gibbs energy of

formations of a molecule at the

• Heat Capacity (ideal gas, at 298K)

- Calculates the heat capacity of a

molecule at the stated conditions.

• Lipophilicity, logP> - Calculates

logP given several algorithms.

• Liquid Viscocity (at 298K) -

Calculates the liquid viscocity of a

• Molar Refractivity> - Calculates

the molar refractivity of a molecule

given several algorithms.

• Normal Boiling Point - Calculates

the normal boiling point of a

• Normal Freezing Point - Calculates

the normal freezing point of a

• Topological Polar Surface Area -

Calculates topological polar surface

area (TPSA).

• ADME Filters> - Contains descriptors

that assess bioactivity.

36

• Bioavailability Score - Calculates

the Bioavailability score.

• Egan Violations Count - Calculates

the number of violations to Egan’s

rules.

• Lipinski’s Rule of 5 Violations

Count - Calculates the number of

violations to Lipinski’s rule of 5.

• Veber Violations Count -

Calculates the number of violations

to Veber’s rules.

• Generate Line Notation> - Contains

functions for generating line notations of

selected structures.

• SMILES - Generates simplified

molecular input line entry specification

(SMILES).

• SLN - Generates Sybyl Line Notation

(SLN).

• InChI - Generates the international

chemical identifier (InChI).

• ROSDAL - Generates the

representation of organic structure

descriptions arranged linearly

(ROSDAL).

• Parse IUPAC Name... - A text field will

appear. Type or paste in a correct IUPAC

name and the structure will be generated

and inserted into the current document.

• Abbreviations> - Contains functions for

maintaining ChemDoodle’s abbreviations

database.

• Add New... - Pops up a window to add

a new abbreviation to ChemDoodle’s

abbreviations database.

• Manage Recognized... - Pops up a

window to add, edit and delete

abbreviations from ChemDoodle’s

abbreviations database.

• Manage My Templates... - Contains

functions for maintaining ChemDoodle’s

templates database.

Reaction Menu

• Clean - Clean the selected reaction. The

reaction must first be defined using the

Build Implied Reaction or Edit

Reaction... functions. This function will

align and distribute the reaction as well as

beautify the reaction arrow. Settings to

control how reactions are cleaned can be set

in the Preferences window, under the

Visuals tab, under the Reaction tab.

• Build Implied Reaction - When an arrow

and structures are selected, this function

will become enabled. All selected structures

with midpoints to the left of the arrow

midpoint become reactants while all

selected structures with midpoints to the

right of the arrow midpoint become

products.

• Edit Reaction... - Will open up a window

showing all the structures in the current

document. Click and drag structures from

the document tray to the reactant and

product trays to explicitly define the

reaction. This function is enabled when an

arrow is selected.

• Dissolve Reactions - Will dissociate any

selected reaction data structures.

Spectrum Menu

• View XY Data - View the XY plot data of

the first selected spectrum. You can copy

and paste this data into other programs, like

Excel.

37

• Edit Perspective... - Will open up a

window showing several tools for editing

the spectrum view and axis. Once closed,

the spectrum in the document will update.

• Expand Perspective - Will expand the

spectrum perspective to view the entire

domain and range of the plot. This function

is enabled when a spectrum is selected.

• Generate> - Contains various functions for

generating and simulating spectra.

• 1 H NMR - Generate a proton nuclear

magnetic resonance spectrum of the first

• 13 C NMR - Generate a carbon-13

nuclear magnetic resonance spectrum of

the first selected structure.

• Mass Parent Peak - Generate a mass

parent peak from the mass spectrum of

the first selected structure. This will

show the magnitude of the parent ion

and the isotopic distribution.

Window Menu

• Minimize - Iconify the main ChemDoodle

window to the dock or system tray.

ChemDoodle’s menu bar will remain

focused on Mac OS X.

• Zoom - Expand the ChemDoodle window

to fill the entire screen without overlapping

any docks or system trays.

• Select Tab Right - This function is enabled

if there are one or more tabs present in the

tab tray. This function will select the tab to

the right of the currently selected tab. If the

currently selected tab it the right-most tab,

then the first tab is selected.

• Select Tab Left - This function is enabled if

there are one or more tabs present in the tab

tray. This function will select the tab to the

left of the currently selected tab. If the

currently selected tab it the left-most tab,

then the last tab is selected.

• Save Document Settings... - Set the

currently defined document settings as the

default document settings.

• Default Workspace - Return the

configuration of windows within the main

ChemDoodle window to the default layout.

• Revert Workspace - Revert the

ChemDoodle workspace to the last saved

workspace.

• Save Workspace - Save the current

configuration of the windows within the

main ChemDoodle window. This also saves

file chooser paths and other workspace

settings. This function is automatically

performed when ChemDoodle is closed.

Purchase Menu

This menu is only present during the free

trial, and is removed when ChemDoodle is

activated with a purchased activation code.

• Activate ChemDoodle - Displays the

activation form to input a purchased

activation code and generate the license for

the ChemDoodle application.

• Buy an Activation Code - Opens the

default internet browser to the purchase

page of the ChemDoodle website.

Help Menu

and your license expiration, if any. This

38

menu item is in the ChemDoodle menu on

Mac OS X.

• ChemDoodle User Guide - View this user

guide in the program most appropriate for

opening PDF files.

• ChemDoodle Keyboard Shortcuts - View

a cheat sheet for all keyboard shortcuts and

actions available in ChemDoodle in the

program most appropriate for opening PDF

files.

• References - View an organized list of

references for the data and algorithms used

in ChemDoodle. You can use this list to

assess ChemDoodle’s quality.

• View User License - View the user license

that you accepted when you activated

• Deactivate ChemDoodle - ChemDoodle

can only be used on the number of

computers determined in your license. To

switch from one computer to another, use

this function first. This function is also

useful if you need to reinstall your

operating system.

• Contact Customer Service - Open the

iChemLabs customer support form and prepopulate

fields. This is the preferred way to

contact iChemLabs customer service.

• iChemLabs Newsfeed - View the

iChemLabs newsfeed RSS.

• Check for Updates - Check for updates to

ChemDoodle. If any are found, you will see

the changes listed and you will be requested

to update ChemDoodle. If allowed,

ChemDoodle will automatically update

itself. There is no need to redownload or

reinstall ChemDoodle for updates.

Toolbars are located at the top-left of the

ChemDoodle window. They contain buttons

for changing how mouse gestures affect

documents, such as placing bonds or placing

a rectangle. There are also buttons for quickly

accessing menu items.

Toolbars can be moved at any time. They will

automatically lock to the borders of the main

ChemDoodle window and to their original

position. To save the current placement of

toolbars so they will remain in that position

when you next open ChemDoodle, select the

Save Workspace menu item in the Window

menu. The placement of toolbars will also be

saved when the ChemDoodle application is

There are 8 toolbars:

• Files + Formatting - Contains buttons for

saving files, transferring content and

formatting fonts and scale.

• Content - Contains functions for

manipulating content including the selection

tools.

• Strokes - Contains 3 drop down selections

for defining bond stroke brush styles.

• Labels - Contains preset labels that can be

used on atoms as well as the Atom Label

tool which will allow you to type whatever

content you would like in atom labels.

• Rings - Contains buttons for drawing

common ring types.

• Bonds - Contains buttons for accessing all

bond types in ChemDoodle.

• Arrows - Contains 3 drop down selections

for defining arrows and buttons for drawing

39

the defined arrow with several preset arc

angles.

• Orbitals - Contains various orbital graphics

for standalone figures or for attaching to

• Shapes - Contains any remaining buttons,

including shapes, carbon chains, brackets,

pens, glassware clipart, text, etc.

Additionally, there are also text formatting

toolbars that will appear when convenient,

such as when editing text areas.

Group Buttons

In some cases, similar buttons are grouped

into a single unified group button. These

group buttons are decorated with a small

highlighted triangle at the bottom-right of the

button. Clicking on the button will select it

and perform the displayed function as one

would expect.

To change to a different function of the group

button, click down and hold the button for

one second or click down and drag slightly to

expand the group button as is shown in Figure

1.13. Once expanded, just drag the mouse

pointer over the function you would like to

use and release the mouse. The function the

mouse was over when it was released will

become selected and will now display as the

main function of the group button.

Figure 1.13: An expanded group button.

Files + Formatting Toolbar

Figure 1.14: Files+Formatting Toolbar

➡Create a new blank document

➡Create a new blank formatted

document

➡Open a file

➡Save a file

➡Print document

➡Print preview

➡Cut

➡Copy

➡Paste

➡Font family (font functions affect

selected content only)

➡Font size

➡Bold font

➡Italicize font

➡Quick Colors button

➡Color button and

color selection button

➡Document scale

➡Zoom In

➡Zoom Out

40

Content Toolbar

Figure 1.15: Content Toolbar

➡Lasso selection tool

➡Rectangular Marquee selection

tool

➡Lasso only Shapes selection tool

➡Rotate in 3D tool

➡Eraser tool

➡Clear tool

➡Add/Remove Hydrogens

➡Clean Structure

➡Clean Reaction

➡Conform to Document Settings

➡Fragmentation Tools

➡Undo

Strokes Toolbar

Figure 1.16: Strokes Toolbar

➡Stroke Style

➡Stroke Width

➡Texture Magnitude

Labels Toolbar

Figure 1.17: Labels Toolbar

The labels toolbar contains the element

labels: H, C, N, O, F, P, S, Cl, Br and I. It also

41

contains the superatom labels: Ac, Bz, Ph,

Me, Et, R and M. Clicking on any of these

labels will change the cursor to that label and

then clicking on an atom will change that

atom’s label to the selected label.

The middle of the toolbar contains the Set

Atom Label tool . The atom label tool,

when selected, will allow you to click on any

atom and open a text field. Type in anything

you want into the text field and then click on

the page or press the return key to close the

text field, setting the selected atom’s label to

the contents of the text field.

Rings Toolbar

Figure 1.18: Rings Toolbar

Clicking on any ring will change the drawing

mode to place rings.

Rings include, from top-left to bottom-right:

• cyclopropane ring

• cyclobutane ring

• cyclopentane ring

• cyclohexane ring

• cycloheptane ring

• cyclooctane ring

• cyclobutadiene ring

• cyclopentadiene ring

• benzene ring

• cycloheptatriene ring

• cyclohexane chair conformer 1

• cyclohexane chair conformer 2

Bonds Toolbar

Figure 1.19: Bonds Toolbar

Just click any bond type and the drawing

mode will change to place bond orders of that

type. Clicking on a bond will change that

bond’s current bond type to the selected bond

type.

The single bond order will add to other bond

orders by default. So clicking on a single

bond will change it to a double bond, clicking

on a double bond will change it to a triple

bond, etc. Clicking on a sextuple bond will

change it to a single bond. Clicking on

decorated bond orders (protruding,

ambiguous double, etc.) will convert it to a

non-decorated (single, double, etc.) bond

before incrementing it. To stop single bond

42

orders from adding to bonds, you can set the

single bond behavior to instead override other

bond orders in the Preferences window under

the General tab.

Bond types include, from top-left to bottomright:

• Zero Order/Ionic bond

• Half bond

• Zigzag bond

• Wavy bond

• Single bond

• Bold Dashed bond

• Bold Single bond

• Bold Hollow bond

• Resonance bond

• Recessed bond

• Protruding bond

• Double bond

• Double Dashed bond

• Bold and Thin Double bond

• Ambiguous Double bond

• Triple bond

• Quadruple bond

• Quintuple bond

• Sextuple bond

• Two Electron bond

• Covalent bond (coordinate covalent by

default, can be changed to a polar covalent

bond)

• Any Order bond

• Unknown Order bond

Arrows Toolbar

Figure 1.20: Arrows Toolbar

The top row of contains three drop down

selections. The first defines the style of the

start arrow, the second defines the style of the

connector between arrows and the third

defines the style of the end arrow. The first

five buttons beneath the drop down selections

allow you to place the arrow in the document

and will preset a given angle. The preset

angles include (from left to right): 270°, 180°,

120°, 90° and 0°. At any time, you can

change the arc angle of a placed arc to any

arbitrary angle of your choice.

The last button is the special arrow presets

button. This group button contains presets for

common non-standard arrow types, such as

retrosynthetic arrows. The arc angles of these

arrows cannot be changed.

Orbitals Toolbar

Figure 1.21: Orbitals Toolbar

The orbitals toolbar contains two rows of

orbital types that can be placed into figures

and attached to structures. From top-left to

bottom-right are Atomic s, Atomic px|y|z,

Atomic dxz|yz|xy|x 2 -y 2 , Atomic dz 2 , Atomic fxz 2 |

43

xy 2 |x(x 2 -3y 2 )|y(3x 2 -y 2 ), Atomic fz 3 , Hybrid sp 3 ,

Hybrid sp lobe, Bonding σ and Bonding π.

Each button is a group button containing

different shading an fill options for that

orbital shape.

Shapes Toolbar

Figure 1.22: Shapes Toolbar

The shapes toolbar contains many group

buttons and other functions for changing the

current drawing mode to place both chemical

and non-chemical objects.

The tools include, from top-left to bottomright:

• Lines - Straight, dotted, wavy and zigzag.

• Arcs - 90°, 120°, 180° and 270°.

• Ovals - Plain, dotted, shadowed and

shaded.

• Rectangles - Plain, dotted, shadowed,

shaded, plain rounded, dotted rounded,

shadowed rounded and shaded rounded.

• Brackets - Square (pair), parenthesis (pair),

curly (pair), chevrons (pair), dynamic

brackets, square, parenthesis, curly,

chevron.

• Chemical Attributes - increment charge,

add radical, positive dipole, single electron,

radical cation, decrement charge, remove

radical, negative dipole, electron pair,

radical anion and electron pair (bar).

• Carbon Chains - 120° Carbon chains,

Fisher Projection chains and Random

Carbon chains.

• Sequence Tool - Draw an amino acid

sequence.

• Polylines - Pen, pen-poly tool and polyline.

• Rulers - Place a measurement ruler.

• Text Areas - Place a text area with a

background and border that can be resized

44

to any dimension and is associated with text

formatting tools.

• Glassware Templates - Opens the

laboratory glassware templates window to

build diagrams with glassware clipart.

Interface Options

In addition to being a very powerful

application for your chemical data,

ChemDoodle is also very customizable so

you can fit its behavior to your preference.

ChemDoodle provides many options for

changing the way it looks, how it works, and

the visual effects that you will see.

To access the interface options, select the

Preferences... menu item in the Edit menu

(in the ChemDoodle menu on Mac OS X).

The first tab, General, will contain the

interface options.

Drawing Controls

Drawing Mode

There are two drawing modes, Quick and

Control. Quick mode will do a complete

multistep-action in a mousedown-dragmouseup

procedure, while Control mode will

complete a multistep-action in a click-moveclick

procedure. The default is Quick mode.

Optimize Zone Size

The Optimize Zone is a special component in

ChemDoodle to help you place bonds in the

optimal position around atoms. It is the blue

circle that appears when placing bonds and

other molecule fragments. To use the

Optimize Zone, just place the mouse pointer

in the blue circle. The bond or fragment being

placed will automatically be oriented in the

most optimal position. You can change the

size of the optimize zone to be Small,

Medium or Large. It is Medium by default.

Hover Distance

The hover distance controls how close the

mouse pointer must be to an object for it to be

considered hovered. The default is 10 pixels,

but you can make this shorter or longer

depending on your preference.

45

Snap to Grid

By default, coordinates for all objects can be

placed anywhere. However, you can set a 5

pixel or 10 pixel grid for objects to snap to.

Single Bond Behavior

By default, Single bonds will increment bond

orders. So using the Single bond tool, if you

click on a Single bond it will become a

Double bond and so forth. However, you can

change this behavior to instead override bond

orders so any bonds clicked on with the

Single bond tool become Single bonds.

Label Behavior

Label tools can either edit the atom clicked on

or add a new bond connected to the atom

clicked on with the new atom having that

label. By default, atom label tools will modify

the selected atom.

Auto-connect Rings and Templates

This option is enabled by default and will

have the atoms placed by ring and template

tools automatically merge with any

overlapping atoms present in the document.

Fix Bond Lengths

This options is enabled by default and fixes

the bond lengths of the drawing tools. You

can quickly reverse this setting when drawing

by holding down the shift key.

Fix Bond Angles

the bond angles of the drawing tools. You can

quickly reverse this setting when drawing by

holding down the alt key.

Require Starting Atom

Many chemical sketchers have the bond as

the smallest building block. ChemDoodle

uses atoms as the smallest building blocks,

and all drawing functions require a starting

atom. You can disable this requirement and

allow new bonds to be placed with a single

mouse click.

Rotate Atom Text with Structures

By default, text will not rotate when you

rotate structures. This way text is always

horizontally readable. You can enable this

setting to have atom text rotate when you

rotate structures.

Bonds are Focusable

If you are working with only atoms or you

don’t want to touch bonds, enabling this

setting will make editing easier. When

enabled, bonds cannot be hovered or selected.

3D Rotation Mode

When using the structure perspective tool,

mouse movements will correspond to X and

Y axis movements during 3D rotation. You

can change this to correspond to a quaternion

rotation if you are more familiar with that

behavior.

Appearance

Recently Opened Files

Recently opened files can be displayed at the

bottom of the File menu, or in a submenu in

the File menu. By default they are displayed

in a submenu, but you may wish to switch

this option for quicker access if you have a

tall screen.

Interface Font

If you prefer a different font from the

standard sans-serif font that ChemDoodle

uses, you can change it in the Preferences

window under the General tab in the

Appearance section. This is also helpful if

you need to switch to a different font that

supports characters for another language.

Interface Color

If you prefer a color other than the default

light green color, you can choose to change

this in the Preferences window under the

46

General tab in the Appearance section.

Light, pale color choices are easiest on the

eyes and are least distracting.

Decorations

Show Unfixed Drawing Measurements

When enabled, statistics are rendered to show

you lengths and angles if they are not fixed.

Show Transform Measurements

you how your lasso functions are altering

your figures.

Lassoing

When enabled, the lasso outline will exhibit a

crawling ants effect so you can easily see it.

View Shimmer Effect on Button Hover

When enabled, buttons will display a

shimmer effect when you hover the mouse

cursor over them. This makes it easy to detect

which button you are pressing.

View Mouse Position on Rules

When enabled, the mouse position will be

ticked on the document’s rulers in red.

View Selection Bounds on Rulers

When enabled, the lasso selection will be

highlighted on the document’s rulers in

amber.

Filechooser Settings

Unified Filechooser Memory

By selecting this option, all filechoosers,

regardless of function will remember the last

location of any of the file choosers.

Otherwise, they will each retain their own

memory.

Include Previews in Filechooser

You may wish to disable this to hide file

chooser previews.

Widgets could be individual applications on

their own, but with ChemDoodle, they

provide added functionality and benefit from

ChemDoodle's useful capabilities.

This section introduces the new user to

widgets within ChemDoodle. It covers the

following topics:

• Identifying the widgets.

• Using the widgets.

• Thorough guides for the widgets.

Widget Windows

Each widget has its own unique interface

contained within a widget window. A widget

window is a simple, movable and resizable

window that contains the widget interface and

other buttons for maximizing and minimizing

the widget as is shown in Figure 2.1 and

Figure 2.2. Widget window decorations will

be slightly different between Windows/Linux

and Mac OS X.

The top bar contains two buttons, one for

minimizing the widget to the ChemDoodle

desktop tray and one for maximizing the

widget to fit the entire ChemDoodle

application window. You can also use the drag

anchors to resize widgets.

To move widgets, just click and drag the top

bar. Widgets will automatically lock to the

borders of the ChemDoodle application and

to their origins.

47

The entire widget interface is presented in the

rest of the widget window below the title,

which is displayed below the top bar.

Figure 2.1: Widget Window on Windows/Linux

Title

Figure 2.2: Widget Window on Mac OS X

Widget Expansion

Some widgets are initially in a collapsed

state. Each collapsed widget will have some

gesture to expand it. For example, the

MolGrabber widget is initially collapsed.

Just type a search term in the text field and

press the return key to expand it as showing

in Figures 2.3-2.4. Every collapsable widget

will also have a collapse button to collapse it.

Figure 2.3: A collapsed widget

Top Bar

Drag

Figure 2.4: An expanded widget

Widget List

There are currently 12 widgets provided in

ChemDoodle:

• Elemental Analysis - Calculates molecular

masses, elemental analysis and isotopic

distributions for structures.

• History - Provides full access to the undo/

redo queue.

• Line Notation Pad - Generates and parses

line notations and will also correct your

input.

• MolGrabber - Search databases for

chemical structures.

48

• Multiplet Tool - Simulate multiplets.

• NMR SignalSeek - Simulate nuclear

magnetic resonance and associate peaks to

nuclei as well as provide more thorough

information about the spectrum and

simulation.

• Properties - Calculates molecular

descriptors.

• Search - Search your computer and

attached storage devices for chemical

• Statistics - Displays document and drawing

statistics.

• Symbols - Quick access to chemically

relevant symbols and the full unicode range.

• Templates - Organizes chemical structure

templates for your use.

• TLC Canvas - Draw thin layer

chromatography plates.

Widget Dock

The Statistics and History widgets are shown

at all times. Only one other widget is shown

in addition to these two at any given time.

You can switch the widget that is shown by

clicking on the widget icon of the widget you

would like to be shown in the widget dock.

The widget dock is located at the bottom-right

of the ChemDoodle window and appears as

shown in Figure 2.5.

Figure 2.5: The widget dock

If you hover over any of the icons, that icon

will be enlarged, and the title of the widget

will appear to the left of the widget dock as

shown in Figure 2.6.

Figure 2.6: Hovering an icon in the widget dock

Just click on the hovered widget icon to select

and show the corresponding widget.

You can also move the widget dock along the

bottom of the application desktop, by pressing

the mouse down and dragging on the (< >)

symbol displayed at the bottom right of the

dock.

Widget Icons

In addition to selecting widgets, these icons

may also perform additional functions. For

instance, if you drag a structure onto the Line

Notation Pad widget icon, that structure will

be loaded into the widget. Information on

these additional functions are provided in the

next sections.

Table 4: Widget Buttons

Button Widget

Elemental Analysis

Line Notation Pad

MolGrabber

Multiplet Tool

49

NMR SignalSeek

Properties

Search

Symbols

Templates

Elemental Analysis Widget

Purpose

The Elemental Analysis widget calculates

several data that are useful to chemists. It

calculates formulas and masses, performs

elemental analysis, and simulates isotopic

distributions.

The interface consists of 4 sections. From top

to bottom, the first section displays the

molecular formula, molecular mass and

monoisotopic mass. The second section

shows the elemental analysis, with each

element shown with its percent composition.

The third section lists the isotopic

distribution, with mass values and intensities.

The fourth section shows an interactive

spectrum of the isotopic distribution.

Figure 2.7: Elemental Analysis Widget

50

History Widget

The History widget is an advanced undo/redo

tool and provides access to the complete log

of all actions performed since the document

was created or opened. Click on a given

action to jump back and forth to the document

state when that action was performed.

The interface consists of a single list in a

scrolling pane as shown in Figure 2.8. The

current state of the document is signified with

a green highlight over the left side of the

latest action. Any actions performed earlier

are undecorated and listed above the current

state, while any actions that have been

undone are highlighted in an amber color and

are listed below the current state. By clicking

on any actions above the current state, the

document will revert back to that action,

undoing all actions between the current state

and the action clicked. By clicking on any

actions below the current state, the document

will redo all actions between the current state

and the action clicked. Therefore, the History

widget allows you to easily revert and restore

any actions performed during the edit history

of the document.

Figure 2.8: History Widget

Line Notation Pad Widget

The Line Notation Pad widget can interpret

and generate SMILES, SLN, InChI and

ROSDAL chemical line notation formats as

well as convert between them with ease. The

interface for the Line Notation Pad widget is

shown in Figure 2.9.

Figure 2.9: Line Notation Pad Widget

The interface, from top to bottom, consists of

a Format drop down selection for choosing

the format, a String text field for inputting

and outputting the line notation, a vertical

row of buttons for performing various

functions, the main structure panel and the

input analysis list. Initially, the interface is

collapsed. Drag a structure onto the Line

Notation Pad widget button or type in a line

notation in the String text field and press the

return key to expand it.

Using the Format drop down selection, you

can choose any of the line notations available

51

to set the current line notation format. If

content is present in the text field, then that

content will be converted into the new format.

The String text field will display the

generated line notation when a structure is

dropped on the main structure panel or the

Line Notation Pad widget button. You may

also explicitly type your line notation in this

component and then press the return key or

the View in 2D button to interpret it and

display the corresponding structure in the

main structure panel.

The buttons perform functions as described in

Table 5.

Table 5: Line Notation Pad Widget Buttons

Button Function

The View in 2D button will

interpret the current string in the

String text field using the format

in the Format drop down

selection and display the

structure in the main structure

panel as well as provide feedback

in the input analysis list.

The Add to the Doodle Board

button will place the current

panel onto the current document.

Alternatively, you can click on

the main structure panel and drag

onto the document to place it.

The Choose Start Point button

will allow you to click on an

atom in the main structure panel

to denote it as the start point for

the generation of the line

notation. Note that if the line

notation format is canonical or if

such an option is set, then setting

the starting point will have no

effect.

The Copy to System Clipboard

as Text will copy the current text

in the String text field onto the

system clipboard as plain text.

For MIME type specific

clipboard contents, set the

appropriate options in the

Advanced tab of the Preferences

window, then copy from the

The Clear button will clear the

current contents and collapse the

widget.

Beside the buttons in the main structure panel

which will display the structure associated

with the line notation in the String text field.

You can generate a line notation for a

structure on the Doodle Board by selecting

the structure and then by clicking and

dragging that structure onto the main

structure panel of this widget. Structures from

the main drawing panel can also be dragged

onto the Doodle Board.

The last component of the interface is a

scrollable list. Any errors or warnings

perceived when interpreting the line notation

will be listed here. Use these suggestions to

help correct malformed strings.

52

MolGrabber Widget

MolGrabber is a web application for

obtaining pre-drawn molecular structures and

properties from online databases. The

interface is shown in Figure 2.10. Currently,

MolGrabber interfaces with the following

databases:

• ChemExper - http://www.chemexper.com/

• ChemSpider - http://www.chemspider.com/

• PubChem - http://

pubchem.ncbi.nlm.nih.gov/

NOTE: Because MolGrabber connects to

online databases, it requires an active

internet connection for use.

Figure 2.10: MolGrabber Widget

a Search text field for inputting a search

term, a Source drop down selection for

choosing the database to search through

followed by a second drop down selection to

restrict the search, a progress spinner to the

right of those three components to notify you

that a search is currently being performed, a

main structure panel with a button column to

the left of it for performing various functions,

a scrollable list to hold all search results and,

at the bottom, statistics about the search result

with traversal buttons for navigating through

large numbers of results.

Initially, the interface is collapsed. Type a

search term in the Search text field and press

the return key to expand it. This can be any

search term that the associated database can

handle. After pressing the return key, the

progress spinner will activate to notify you

that it is performing the search. After the

search completes, the progress spinner will

deactivate, the results will populate the result

list and the first result will appear in the main

structure panel.

The Source drop down selection can be used

to select which database to search. The

second drop down selection will restrict your

search to a specific data field type supported

by the database. Just choose a specific field

and the search will only match results in that

field for the input search term.

Table 6.

Table 6: MolGrabber Widget Buttons

53

The Search button will begin the

search query using the search

term input into the Search text

field and restrict it to matching

the field selected in the Source

drop down selections.

onto the document to place it.

The Show/Hide Hydrogens

button will add and remove

Hydrogens from the structure in

the main structure panel based on

the coordinates for Hydrogens

provided by the database. Some

databases may not provide

Hydrogen coordinates and

therefore this function will have

no effect.

The Show Associated Data

button will display all associated

database data for the structure

displayed in the main structure

panel.

To the right of the buttons is the main

structure panel that will display the structure

for the selected result. After obtaining the

structures you would like to include in your

figures, all you have to do is drag and drop

the structure from the main structure panel

Below the buttons is the search result list.

This list will display a maximum of 20 results

and follows the following format for each

entry:

Name (Molecular Formula) [Molecular Mass amu]

Click on any of the results to display them in

the main structure panel.

Below the search results is a label to inform

you of which search results are presented in

the current result set along with traversal

buttons to navigate through large numbers of

results. Just press the left and right arrows to

view the previous 20 and next 20 results

respectively. If there are no previous or no

next results, then the corresponding arrow

will be disabled.

NOTE: ChemSpider does not currently

support pagination of results, so be careful

with generic queries as they may return

many, many results and may take a long

time to complete.

Directing to the Online Database

After a molecule has been loaded, clicking on

the Show Associated Data button will list

associated data from that database. The top

item will be the specific database id as a

hyperlink. The link will open up your default

browser to the selected database’s page for

the current result.

Database Notes

ChemDoodle only provides an interface to the

databases supported in the MolGrabber

widget. You should inform yourself about the

copyrights, disclaimers and warranty

information provided by these databases

before using them.

ChemExper Disclaimer

54

http://www.chemexper.com/?main=ccd/

disclaimer.html

***** USE AT YOUR OWN RISK *****

ChemExper sprl compiles chemical

information from many sources.

THIS DATA IS PROVIDED "AS IS" AND

IN NO EVENT SHALL CHEMEXPER BE

LIABLE FOR ANY DAMAGES,

INCLUDING, WITH OUT LIMITATION,

DAMAGES RESULTING FROM LOST

DATA OR LOST PROFITS OR REVENUE,

THE COSTS OF RECOVERING SUCH

DATA, CLAIMS BY THIRD PARTIES OR

FOR OTHER SIMILAR COSTS, OR ANY

SPECIAL, INCIDENTAL, OR

CONSEQUENTIAL DAMAGES, ARISING

OUT OF THE USE OF THE DATA.

The accuracy or reliability of the data is not

guaranteed or warranted in any way and the

Providers disclaim liability of any kind

whatsoever, including, without limitation,

liability for quality, performance,

merchantability and fitness for a particular

purpose arising out of the use, or inability to

use the data.

ChemSpider Disclaimer

http://www.chemspider.com/Disclaimer.aspx

General

The ChemSpider website is maintained by

The Royal Society of Chemistry on behalf of

its wholly owned subsidiary RSC Worldwide

Ltd. RSC Worldwide Ltd does not warrant or

assume any legal liability or responsibility for

the accuracy, completeness, or usefulness of

any documents, data, software, apparatus,

product, process, or other information on the

ChemSpider website. You should not rely on

any information on the website for any

assessment of the risks of any specific

experiment, procedure or process that you

wish to carry out; you should always carry

out your own risk assessment for such

purposes. The information on this website

may not be correct or appropriate for local

regulations, legal codes, practices or policies.

The information may be out of date. RSC

Worldwide Ltd takes no responsibility for any

injury, loss, or damage caused in any manner

whatsoever by the use of the information on

this website.

Some ChemSpider webpages link to pages on

other websites, for the convenience of users.

RSC Worldwide Ltd is not responsible for the

availability of content on these webpages.

Nor does it endorse or warrant the services,

products or information offered on these other

pages, unless explicitly stated.

For site security purposes software programs

and algorithms are used to monitor traffic and

to identify unauthorized attempts to upload or

change information or otherwise cause

damage to the ChemSpider service. In the

event of unauthorized activities utilizing

information on the ChemSpider website

information from these sources may be used

to help identify an individual for prosecution.

Data

The data on the ChemSpider website are

sourced from a number of contributors and

collaborators. The majority of data were

originally sourced from the NCBI-PubChem

website and are made available under the

explicit statements and disclaimers provided

by National Center for Biotechnology

Information (NCBI). NCBI places no

restrictions on the use or distribution of the

data contained within their database. RSC

Worldwide Ltd has abided by the assumptions

of NCBI. These are as follows: "While some

submitters of the original data (or the country

55

of origin of such data) may claim patent,

in all or a portion of the data (that has been

submitted), NCBI is not in a position to

assess the validity of such claims and,

therefore, cannot provide comment or

unrestricted permission concerning the use,

copying, or distribution of the information

contained in the molecular databases." In this

regard should any contributors to the NCBI-

PubChem database wish to have their data

removed from the ChemSpider website please

send a detailed request to

[email protected].

Data on ChemSpider, including structures and

spectra, are sourced also from individuals. In

depositing these data to the ChemSpider

website, these individuals undertake that they

have the rights to do so, and that the rights do

not reside with any third party.

PubChem User Requirements

http://eutils.ncbi.nlm.nih.gov/entrez/query/

static/eutils_help.html

Do not overload NCBI’s systems. Users

intending to send numerous queries and/or

retrieve large numbers of records from Entrez

should comply with the following:

• Run retrieval scripts on weekends or

between 9 pm and 5 am Eastern Time

weekdays for any series of more than 100

requests.

• Make no more than one request every 3

seconds.

• NCBI’s Disclaimer and Copyright notice

must be evident to users of your service.

NLM does not claim the copyright on the

abstracts in PubMed; however, journal

publishers or authors may. NLM provides

no legal advice concerning distribution of

copyrighted materials, consult your legal

counsel.

56

Multiplet Tool Widget

The Multiplet Tool widget is a comprehensive

tool for generating multiplet trees, simulating

signals and producing their figures. It is

perfectly suited for simulating nuclear

magnetic resonance (NMR) or electron

paramagnetic resonance (EPR, a.k.a. ESR)

signals. The interface is shown in Figure 2.11.

Figure 2.11: Multiplet Tool Widget

the main multiplet panel and a row of buttons

for performing various functions.

Use the buttons to set up the simulation and

layout of the multiplet. The buttons perform

functions as described in Table 9.

Table 9: Multiplet Tool Widget Buttons

multiplet from the main multiplet

panel into the current document.

The Input Parameters button

pops up a window for you to

define parameters for the

simulation including the number

of neighboring nuclei, their spin

and coupling magnitude.

The Real-Time Sliders button

provides a window with sliders

for each parameter. Changing the

sliders will affect the simulation

in real time.

The Settings button will display

a window to define how the

simulation is performed and how

the multiplet figure is laid out

and displayed.

Once you have completed your simulation,

just drag and drop the multiplet from the main

multiplet panel onto the Doodle Board.

Simulating Multiplets

To simulate multiplets, define the parameters

in the Input Parameters window that

appears after clicking the Input Parameters

button and then click the Calculate button as

shown in Figure 2.12. Press the reset button

in this window to reset all parameters.

Figure 2.12: Multiplet Input Parameters

57

To tweak the input parameters to analyze their

affect on the simulation, just use the Real-

Time Sliders button and change the values

slowly in the window that appears as shown

in Figure 2.13. When you are satisfied with

the simulation, press the Done button. The

Reset button will reset the parameters to their

initial values before the window was opened.

Figure 2.13: Real-Time Sliders

Setting up the Multiplet Figure

To define how the simulation is performed

and how the multiplet figure is displayed,

click on the Settings button to show the

Multiplet Settings window as shown in

Figure 2.14.

Figure 2.14: Multiplet Settings

Board

To edit a multiplet from the Doodle Board,

just select it and then drag and drop it onto

the Multiplet Tool widget button or onto the

main multiplet panel. A copy will be made

and can be edited using the Multiplet Tool

widget. Just add this new edited multiplet to

the Doodle Board and delete the old one.

Memory and Runtime Issues

A nucleus of any spin may be used, including

hypothetical spins, however more complex

simulations require more memory and

processor power leading to longer runtimes.

Some extremely complex simulations may

cause memory issues.

58

NMR SignalSeek Widget

The NMR SignalSeek widget simulates 1 H

and 13 C nuclear magnetic resonance and also

associates peaks with nuclei. Full information

about each simulation is provided for in-depth

analysis. The interface is shown in Figure

2.15.

Figure 2.15: NMR SignalSeek Widget

The interface, from left to right, consists of

the main structure panel and a row of buttons

for performing various functions, followed by

a set of panels for displaying the simulated

NMR spectra with 13 C displayed on top and

1 H displayed on the bottom.

The main structure panel displays the

structure being analyzed and is interactive.

The spectra are also interactive and display

the simulation results. Use the buttons to set

up the simulation and copy content to the

Doodle Board. The buttons perform

functions as described in Table 10.

Table 10: NMR SignalSeek Widget Buttons

button will place both the

simulated 1 H and 13 C spectra

onto the current document.

simulation is performed.

Simulating NMR

To simulate NMR spectra for a structure, drag

and drop that structure from the Doodle

Board onto the NMR SignalSeek widget

button or the main structure panel. The 1 H

and 13 C NMR spectra are instantly generated

All variables for the simulation can be

customized. To define the variables, click on

the Settings button to display a window

containing the parameters, as show in Figure

2.16. When you are finished, click the

Simulate button to recalculate the spectra.

Adjust these parameters to match an

experimental spectrum for correlated figures

on the Doodle Board. Settings include:

• TMS - Display or hide the reference peak.

• Roof Effects - Simulate roof effects.

• Line Shape - Lorentzian or Gaussian.

• Pulse Frequency - The spectrum

resolution. The value is appropriate for 1 H

NMR. 13 C NMR will be simulated to a

resolution of a quarter of this value to

remain consistent with experimental

spectrometers.

• Line Width - Control the line width.

• Dilution - Affect the solvent/solute

intensity ratio.

• Temperature - Change the simulation

temperature.

• Solvent - Choose a solvent. Splitting is

fully calculated with the appropriate spin of

59

the nuclei (Deuterium has a spin of 1 and

you will see this splitting correctly in the

solvent peaks).

Figure 2.16: NMR Simulation Settings

Analyzing the Results

The spectra are completely interactive. You

can easily change the view of the spectrum by

clicking and dragging to zoom in on the xaxis.

Double clicking on the spectrum will

revert it to the full view. Scrolling will change

the scale of the y-axis.

Peaks and nuclei are hoverable. Hovering

over a peak will highlight the corresponding

nuclei and vice versa. The chemical shift of

the nuclei is displayed above the structure in

Clicking on a highlighted peak or nuclei set

will display further data from the simulation,

including the shift prediction, splitting nuclei

and j-constant predictions as shown in Figure

2.17. Use this to gain further information

about multiplets.

Figure 2.17: In-depth Simulation Information

Lastly, the widget is initially small to

conserve space. But with all widgets, you can

resize or maximize them if you would like

more interaction space.

How NMR is Simulated

The simulations in the NMR SignalSeek

widget are based on empirical algorithms,

with a database of incremental constants

compiled from publications and some

unpublished work. These references are listed

by clicking the References menu item in the

Help menu. Further information on the

algorithms used to simulate NMR is provided

in Appendix E.

60

Properties Widget

The Properties widget calculates and

displays descriptors for molecules. There are

two unique interfaces displayed by the

Properties widget depending on the situation.

If and only if a single molecule is being

drawn, a table will be displayed. Otherwise, a

drop-down tree will be presented to show data

for each of the selected molecules. The

Properties widget will automatically update

to reflect any changes if allowed to. The

interface displayed when a single molecule is

being edited is shown in Figure 2.18, and the

interface displayed when molecules are

selected is shown in Figure 2.19.

Figure 2.18: Properties Widget Interface with a

Single Molecule is being Drawn

Figure 2.19: Properties Widget Interface when

Molecules are Selected

The interface consists of a checkbox and

button at the top that control when the widget

updates and the data component at the bottom

which displays a table or drop-down tree

depending on the situation.

The table is non-interactive and only displays

the most important information. For the rest

of the descriptors, select the molecule to

display the organized tree. To use the tree,

just click the arrow to the left of each item, or

double click on the item to expand it.

When the Auto-update checkbox is selected,

the Properties widget will refresh

automatically when any content is changed.

Deselect the checkbox to improve drawing

performance when handling large molecules.

When the Auto-update checkbox is

deselected, the Update button will be enabled

to manually control when the widget

refreshes.

Currently, the Properties widget calculates

the following properties for each molecule:

61

• Molecular Formula

• Counts

• Atoms

• Bonds

• Rings

• Frèrejacque Number

• All Rings

• Hydrogen Bond Acceptors

• Hydrogen Bond Donors

• Degree of Unsaturation

• Wiener Index

• Calculations

• Molar Refractivity

• Topological Polar Surface Area

• XlogP v2.0

• Mass

• Molecular

• Monoisotopic

• Elemental Composition

To copy content from the Properties widget,

just right-click on any item and choose the

Copy menu item.

It may take a lot of clicks to access

information through the Properties widget.

For quicker access to all molecular

descriptors, use the Descriptors submenu of

the Structure menu.

Search Widget

The Search widget allows you to search your

hard drive and any attached storage devices

for chemical structures. The Search widget

recognizes all formats that ChemDoodle

understands, so you will be able to find the

old files you thought you lost a long time ago

and edit them in ChemDoodle. The interface

is shown in Figure 2.20.

Figure 2.20: Search Widget

a Folder button to select the root directory of

the search, Match and Multiple options to

define how the search is performed, a small

drop panel to drop the structures to be

searched for and to notify you that a search is

currently being performed, a column of

buttons for various functions with a main

structure panel to the right of them, a list of

62

search results and then labels to notify you of

search progress.

The top section will allow you to select a root

folder for the search. Just click on the Folder

button and use the file chooser that appears to

select a folder. Try to be as exclusive as

possible when choosing a root folder, as

searching your entire hard drive can take a

very long time and may cause memory issues.

The Match and Multiple options will affect

how the search is performed. Setting Match

to Entire will guarantee that all results are

exact matches of the query structures, while

selecting Substructure will match any

structures where the query structures are

matched exactly or contained within larger

structures. Setting Multiple to AND will

ensure that all query structures are matched in

a file for that file to be considered a result,

while selecting OR will allow any matched

query structure to qualify the file as a result.

Initially, the interface is collapsed. Drag and

drop a structure or group of structures from

the Doodle Board onto the small drop panel

or onto the Search widget button to expand it

and set the query structure content.

Table 7.

Table 7: Search Widget Buttons

search query using the query

structure(s) dropped on Search

widget button and the search

options set.

The Settings button will allow

you to control search parameters

and improve performance.

The Open button will open the

currently selected result on the

While the search is being performed, a

pulsing stop sign will become visible on top

of the small drop panel to notify you of search

progress. Clicking on the stop sign will

terminate the search. At the bottom of the

interface are two labels. The first label names

the file currently being searched, and will

display Finished! when completed. The

second label displays statistics about the files

searched since the search was initialized in

the following format:

Files Matched/Chemical Files Searched/Total Files Searched

Be careful with the search! Searching large

numbers of files may cause ChemDoodle to

run out of memory, causing slow response in

ChemDoodle. Choose the root search folder

and the search settings described in the next

section with care.

Once the search is completed, all matched

files will be listed in the results list. Click on

any result to view all the structures in that

file, one at a time, in the main structure panel.

All hits are highlighted in red. If a file

contains multiple structures, clicking the grey

63

arrows that appear to the left and right of the

structure will allow you to browse through

them. The total number of structures in the

file is noted at the bottom left of the main

structure panel. Once you have found the

structure you were looking for, just drag and

drop the structure from the main structure

panel onto the Doodle Board. You can also

use the Open button to open the entire file on

Search Settings

Search parameters can be defined by clicking

on the Settings button. A window with the

options will appear as shown in Figure 2.21.

Figure 2.21: Search Settings for the Search

There are currently 3 options:

1. Search File Size Restriction - This value

determins the maximum file size that the

Search widget will include in its search,

avoiding memory issues.

2. Maximum Number of Search Results -

This value will control the maximum

number of search results. The search will

continue until all the files in the selected

root search folder are visited or when this

maximum result value is reached. Keeping

it low and providing smaller root search

folders will avoid runtime and memory

issues.

3. Exclude PDB Files - Many times, PDB

files are very large and contain molecular

dynamics trajectories or Monte Carlo

distributions. To avoid all of these files,

which will cause runtime and memory

issues, keep this option selected. If you

need to search through PDB files, turn this

option off.

64

Statistics Widget

The Statistics widget will display information

about the current document and hovered or

selected items. Use it to help with drawing

and placement tasks.

The interface is separated into three sections

as shown in Figure 2.22. The top section

displays information about the document, the

middle section displays information about the

content, and the final section displays specific

information about hovered or selected

Figure 2.22: Statistics Widget

Symbols Widget

The Symbols widget is a complement to the

Labels toolbar. This widget contains an

abbreviation library, a periodic table of

elements, arrows, greek letters and many

other symbols. A few selected tabs are shown

in Figures 2.24-2.26.

The content in the Symbols widget is small

and may be difficult to read. As can be seen in

Figure 2.23, hovering over any symbol will

show a larger preview at the top left hand

corner of the widget. Hovering for a few

seconds will also display a tooltip description.

Figure 2.23: Symbol Preview

When abbreviations or elements are chosen,

you may modify atoms as described in the

labels section. Other symbols, such as arrows

may not be used directly as atom labels.

However, you can open up an atom label text

field, and then input the symbol. If you are

modifying any text component, clicked

symbols will be inserted into the component's

65

Figure 2.24: Abbreviations Tab

Figure 2.25: Arrows Tab

Figure 2.26: Elements Tab

If you set an atom's label to one that is not

recognized or parsed by ChemDoodle, an

unrecognized warning will appear. You may

dismiss this warning or edit the current list of

abbreviations to allow unrecognized tokens

by selecting the Add New... menu item in the

Structure menu in the Abbreviations

submenu.

Figure 2.27: The Unicode Character Selector

All possible symbols available are accessible

in the Symbols widget, even if they are not

displayed immediately in the tab sets. Just

click the Unicode Character Selection

button at the bottom of the widget to view the

unicode character selector shown in Figure

2.27. Using hex, you can traverse the entire

Unicode range and easily insert any desired

symbols into text components. Note that not

all fonts will have character glyphs assigned

to each hex value. In these cases, a blank

space or empty rectangle will appear in your

text component and in the unsupported

symbol button.

NOTE: Some programs use the Symbol

font to display symbols. This is an archaic

66

solution and the standard is to now use

unicode characters, which ChemDoodle

fully supports. ChemDoodle will try to

recognize and correct such cases when

reading in files from other programs.

Templates Widget

The Templates widget organizes your

templates and allows you to easily use them.

The interface is shown in Figure 2.28.

Figure 2.28: Templates Widget

a main structure panel, a drop down selection

for selecting a template group and a scrollable

list for selecting a template.

The main structure panel displays the selected

template. An atom can be set to be the

substitution point by clicking on it. The

substitution point is the atom that will be

overlapped with the atom the template is

connected to.

The template group drop down selection will

allow you to select a group of templates to

browse. After selecting a template group, the

template list will populate with templates

from that group. Just click on a template to

display it in the main structure panel for use.

67

Using Templates

Drawing with templates and creating

templates is discussed in detail in Chapter 3.

TLC Canvas Widget

The TLC Canvas widget provides a tool for

creating graphics of thin layer

chromatography (TLC) plates. The interface

is shown in Figure 2.29.

Figure 2.29: TLC Canvas Widget

The interface, from left to right, consists of a

column of buttons for spot types, the main

TLC panel for drawing the TLC plate and a

column of buttons for performing various

functions.

The top button in the spot type column sets

the color of spots. Beneath the color button

are 6 different shapes of spots:

• Compact Spot - a small dot

• Expanded Spot - a circle

• Trailing Spot - a small dot with a trail

• Widened Spot - an oval aligned

horizontally

68

• Crescent Spot - a crescent shape with bowl

facing downwards

• Custom Spot - a splatter shape that can be

changed

Click on any of the spot types to set the

drawing mode to place the spot.

Each spot button is a group button. Expand

the group button for more spot styles. For

each spot there are three spot styles:

• Solid Style - Solid throughout

• Empty Style - Just a line border

• Diffuse Style - Gradient from the center to

the edges

The main TLC panel contains the TLC plate

being drawn. You can edit it using the

controls to the right. When finished editing

the TLC plate, use the Add to Doodle Board

button to place it on the Doodle Board.

The right-most button column contains

function buttons to control how to edit the

TLC plate. The buttons perform functions as

described in Table 8.

Table 8: TLC Plate Widget Buttons

button will place the current TLC

plate in the main TLC panel onto

The TLC Settings button will

popup a window to edit the

visual specifications of the TLC

The Move button allows you to

translate spots along their lanes

and allows you to move the

origin and solvent front.

The Resize Spots button will

display the anchor points for all

spots and allow you to click and

drag them to alter spot shapes.

The Delete button will all you to

remove spots by clicking on them

and allow you to delete lanes by

clicking on the lane tick at the

origin.

The Clear button removes all

spots, leaves a single lane, and

resets the origin and solvent

front.

Drawing TLC Plates

There are 13 buttons associated with the TLC

Canvas. The controls on the left are the

simplest. The top button is the color of the

spots, just click it to choose a different color.

The rest of the buttons in that column

correspond to spot shapes. These are the

compact, expanded, trailing, widened,

crescent and custom spots, in that order. Just

click on a spot button, then hover over the

TLC plate for a preview and Rf calculation.

Once you are satisfied with a location, click

to place the spot. You can create new lanes by

placing spots in between the existing lanes.

These spot buttons are group buttons and

more spot styles will appear when hovered.

All of the spots can be initialized with a solid,

hollow or gradient style. The gradient styled

spots most closely represent actual spots.

69

Using the Move button, you hover over spots

to highlight them, and then click and drag to

move them along their lanes. Rf values are

displayed while you move spots. You may

also click and drag the origin and solvent

front to move them, preserving Rf values.

When spots are hovered, you can right click

on them to open a popup menu with the

following functions:

• Duplicate Spot - Will produce a duplicate

spot of the hovered spot, underneath the

hovered spot in the same lane.

• Remove Spot - Will delete the spot.

• Format Spot - Opens the Format Spot

window.

The Format Spot window will provide several

options for precisely defining its color, style,

display settings and position as shown in

Figure 2.30.

Figure 2.30: Format Spot Window

To resize and reshape spots on the TLC plate,

use the Resize Spots button. Just hover over

the control points that appear, and then click

and drag to move them. All spots except the

custom spot are defined by 4 control points.

You may move all four to create different

shapes. The custom spot is unique and is

defined by 8 control points. You may use

custom spots to create much more

complicated shapes.

To remove spots and lanes, use the Delete

button. Hover over spots to highlight them,

then click to remove them. You may delete a

lane by clicking its lane tick at the origin.

Deleting a lane will also delete its contained

spots. To clear and reset the entire TLC plate,

click the Clear button.

To edit a TLC plate from the Doodle Board,

just select it and then drag and drop it onto

the TLC Canvas widget button or onto the

main TLC panel. A copy will be made and

can be edited using the TLC Canvas widget.

Just add this new edited TLC plate to the

Doodle Board and delete the old one.

Chapter 3: Basic

Structures

You can draw any structure imaginable with

ChemDoodle. However, with all of the

drawing tools available, drawing basic

structures may seem overwhelming to the

new user.

basic structure drawing tools within

ChemDoodle. It covers the following topics:

• Recognizing the structure drawing tools.

• Drawing atoms.

• Setting atom labels.

• Drawing bonds.

• Changing bond orders.

• Drawing chains.

• Drawing rings.

• Drawing templates.

• Adding attributes to structures, such as

charges, radicals and symbols.

• Setting mass number values to isotopes.

• Placing orbitals on structures.

KeyBoard Shortcuts

There are many keyboard shortcuts to help

you draw structures quickly and efficiently.

The full list of keyboard shortcuts is given in

the KeyboardShortcuts.pdf file located in the

docs folder in the main ChemDoodle

installation folder.

71

Atoms

Atoms are the basic building blocks in

chemistry and are the basic building blocks in

ChemDoodle. Before any other chemical

objects can be drawn, an atom must be

present as the starting point.

Placing Carbon Atoms

When you first use ChemDoodle, you will

notice a gray dot following your mouse

pointer on the Doodle Board as shown in

Figure 3.1.

Figure 3.1: Trailing Carbon Atom

To set a carbon atom at the current location of

the mouse pointer, just click the mouse. This

will set the carbon atom and structures can be

grown from it.

At any time while drawing chemical

structures, if there is no hovered atom to grow

from, a carbon atom will trail your mouse to

be placed and grow a new structure.

NOTE: More advanced users may find it

inconvenient to always require a starting

atom to draw structures. You can turn off

this restriction in the Preferences window

under the General tab, by check the

Require Starting Atom checkbox. Clicks

with the bond tools will then immediately

place those bonds and ring, templates and

chains will not require a starting atom.

Placing Other Elements

To place atoms with element symbols other

than carbon, use the Labels toolbar or the

Elements panel in the Symbols widget. Just

click on the desired element symbol, and the

mouse cursor will change to be that symbol

with a small arrow at the bottom-left. Once

you have located where to place the atom

using the bottom-left arrow of the new mouse

cursor, just click to place it.

If you click while an atom is hovered, then

that atom’s label will change to the currently

selected element symbol.

Labels

To place atoms with any text you desire, click

on the Set Atom Label tool located in

the Labels toolbar. Then click on the Doodle

Board in the desired location to place the

new atom and to open up an atom label text

field. Type in the desired atom label text into

the text field and then click elsewhere on the

Doodle Board or press the return key to close

the text field and set the atom.

If you click while an atom is hovered, then a

text field will appear for that atom’s label for

you to edit.

Hovering Atoms

With most tools in ChemDoodle, atoms can

be hovered. Exceptions include the shape

tools, such as when drawing rectangles.

Hovering an atom is very simple, just get

your mouse close enough to an atom so that it

is surrounded by an amber circle as shown in

Figure 3.2.

Figure 3.2: A Hovered Atom

The atom is then defined as being hovered

and further actions pertaining to it can be

performed.

72

By default, most carbon atoms have their

labels hidden to create skeleton figures. To

modify when carbon labels are displayed,

please refer to the Carbon Labels section in

Selecting Atoms

To select atoms, first hover them and then

press the mouse down. The amber circle will

turn into a blue circle as shown in Figure 3.3.

Figure 3.3: A Selected Atom

The blue circle is actually a special

component called the Optimize Zone, which

will be discussed in the Bonds section.

To deselect atoms, just release the mouse.

Elements

To change an atom’s label to another element

symbol, use the Labels toolbar or the

with a small arrow at the bottom-left. Once

you have hovered the atom with the label to

be changed, just click to set the new label.

Additionally, when an atom is hovered, you

can press any of the letter keys on the

keyboard to cycle through the element

symbols that begin with that letter.

Text

To change an atom’s label to any text you

desire, click on the Set Atom Label tool

located in the Labels toolbar. Then hover the

atom with the label to be changed and click to

open up its atom label text field. Type in the

desired atom label text into the text field and

then click elsewhere on the Doodle Board or

press the return key to close the text field and

set the new label.

Additionally, you can hover the atom in any

mode and then press the space key to open

the atom’s label text field.

for other Atoms

When writing a complex atom label, you may

want to repeatedly use that label for other

atoms. After typing the label, just hover the

other atoms with labels to be changed and

press the enter key. The hovered atom’s label

will be set to the last typed label.

You can also define the label text to be used

by the enter key by opening up a previously

typed atom label text box and then closing it.

Moving an Atom

To move an atom, first select one of the

selection tools discussed in Chapter 5. Make

sure that no content is currently selected by

emptying the lasso. Perform the following

steps:

1. Hover the atom to be moved.

2. Press the mouse down to select the atom.

3. Drag the mouse to move the atom.

4. Release the mouse to finish the move

action.

If the atom is a terminal atom in a molecule,

then the above instructions will move the

73

atom and bond with fixed angles and lengths

as described in the Bonds section.

If the atom is part of a molecule and not a

terminal atom, the the above instructions will

move that entire molecule. Just hold down the

shift key while performing the above

instructions to move the atom by itself.

Deleting an Atom

To delete an atom, hover it and then press the

delete or backspace key. All attached bonds

will also be removed, leaving the adjacent

Chemical Labels

The last section described how to use the

atom label tool to assign any arbitrary text to

an atom. This text is chemically interpreted; a

label of CH3 will be interpreted as one carbon

atom with three hydrogen atoms attached to

it. Much more advanced labels can be written

and parsed. More information on chemical

interpretation, and expanding these labels, is

described in Chapter 6.

In addition to chemical interpretation, the

label will automatically be formatted for

display; the CH3 label will display as CH3.

Stacking will also be applied, so as bond

overlap with labels is kept to a minimum.

ChemDoodle’s intuition may not always be

what you intended though, and you may want

to format more advanced labels, such as for

rendering isopropyl groups (iPr and i Pr) or

adding indexes to carbon chain groups (R 10 ).

In these cases, you can override

ChemDoodle’s chemical interpretation and

apply your own formatting.

Atom Label Tool

When opening an atom label field, a format

toolbar will appear above it containing

several controls. The only enabled button will

e the Interpret Chemically button, which is

selected by default as shown in Figure 3.4.

Figure 3.4: Only one button is enabled by default.

Without further editing, closing this label will

assign an ethyl group to the atom and the text

will be automatically formatted as CH2CH3.

Atom Label Token Stacking

When labels are chemically interpreted, they

will be split up into tokens that describe each

discrete unit. For instance, NH will be split

into (N)(H) and CCH2COOH will be split

into (C)(CH2)(COOH). More about this is

covered in Chapter 6. ChemDoodle will

automatically stack tokens in atom labels

such that they overlap with surrounding

bonds as little as possible as shown in Figure

3.5.

Figure 3.5: Atom label tokens are stacked to

overlap with bonds as little as possible.

By default, if not on a terminal atom, and

stacking will help reduce clutter, the second

token and all subsequent tokens will be

stacked to the next line. There are two visual

specifications for more precise control over

this behavior:

• Stack Lone/Terminal - In the Preferences

window, in the Visuals tab in the Atoms

section under the Labels subsection, you

can set this checkbox to determine if lone

and terminal labels will also stack labels.

74

• Token Stacking - In the Preferences

can set multi-choice option to declare

whether token stacking occurs for all

individual tokens, for only the second token

or never for any token.

In addition to the token behavior settings, you

also have full control of the spacing between

tokens. All of these settings are present in the

Preferences window, in the Visuals tab in the

Atoms section under the Labels subsection.

Formatting Atom Labels

If a different format is desired, just deselect

the Interpret Chemically button and the

formatting options will be enabled as shown

in Figure 3.6.

Figure 3.6: Applying a custom format to an atom

label.

Use the controls in the toolbar that appears

above the atom label field to explicitly format

the atom label. Table 11 lists how to change

the following attributes.

Table 11: How to change these formatting

attributes

Attribute Control

Bold Select the text to be bold

and press the Bold button.

Italics Select the text to be

italicized and press the

Italic button.

Underline Select the text to be

underlined and press the

Underline button.

Strikethrough Select the text to display

the strikethrough and

press the Strikethrough

button.

Superscript Select the text to be

superscript and press the

Superscript button.

Subscript Select the text to be

subscript and press the

Subscript button.

Alignment The entire label will be

aligned to the selection of

the Align Left, Align

Center or Align Right

buttons.

Color Select the text to be

colored and press the

Choose Color button.

Then select the color.

Font Family Select the text to change

the font family of and then

use the font chooser in the

Format toolbar to select

the font family.

Font Size Select the text to change

the font size of and then

use the size chooser in the

the font size.

Note: When disabling chemical

interpretation, the label will lose all

chemical significance, and will not be

expandable or suitable for any chemical

75

Atom Label Orientation

By default, atom label tokens will orient

themselves in the direction of least overlap

with the rest of the structure. Some times, it

may be necessary to force the label to flush in

a specific direction. To do so, perform the

1. Hover the atom with label to orient.

2. Right-click on the atom and expand the

Label Flush submenu.

3. Choose the direction to orient the label.

Choose Auto if you want ChemDoodle to

automatically determine the best

orientation.

Bonds

Bonds are the second most important building

blocks in chemistry. Bonds in ChemDoodle

are graphical connectors between atoms.

There are many options for bond types and

for defining how they look.

Placing a Single Bond

To place a single bond, click the Single Bond

tool in the Bonds toolbar which should

be selected by default when ChemDoodle is

opened.

Then hover over an atom and press the mouse

down. A preview of the new bond and atom

will be drawn as shown in Figure 3.7.

Figure 3.7: New Bond Placement Preview

Drag the mouse and use the techniques

discussed in the following subsections to

place the bond in the preferred orientation.

Then release the mouse to set the bond.

To place bond types other than Single bonds,

just click on the desired bond type in the

Bonds toolbar. Then follow the instructions

for placing a Single bond.

Optimize Zone

most optimal position.

The Optimize Zone size can be changed in

the Preferences window under the General

tab.

Placing Bonds with Fixed Lengths and

Angles

By default, fixed widths and fixed angles are

enforced when drawing structures. To place a

bond within these restraints, hover over an

atom and press the mouse down with a bond

tool. You will see the Optimize Zone appear.

Drag the mouse pointer out of the Optimize

Zone. The new bond placement will now

orient towards the mouse pointer.

The default fixed length is defined by the

Bond Length visual specification in the

Preferences window under the Visuals tab

under the Bonds tab. Angles are fixed every

30° starting at 0°.

You can set whether fixed lengths and/or

fixed angles are on by default in the

Preferences window under the General tab.

76

When placing bonds outside of the Optimize

Zone, fixed lengths will be enforced. To

break from fixed lengths, hold down the shift

key while placing the bond.

You may turn off fixed lengths in the

In this case, the shift key will then enforce

fixed lengths.

Placing Bonds at Non-fixed Angles

Zone, fixed angles will be enforced. To break

from fixed angles, hold down the alt key

while placing the bond.

You may turn off fixed angles in the

In this case, the alt key will then enforce

fixed angles.

and Non-fixed Angles

Zone, fixed angles and fixed lengths will be

enforced. To break from fixed lengths and

fixed angles at the same time, hold down both

the shift and alt key while placing the bond.

You may turn off fixed lengths and fixed

angles in the Preferences window under the

General tab. In this case, holding the shift

and alt keys will then enforce fixed lengths

and angles.

Hovering Bonds

With some tools in ChemDoodle, bonds can

be hovered. Hovering a bond is very simple,

just get your mouse close enough to the

center of the bond so that it is encapsulated by

a pair of amber semicircles as shown in

Figure 3.8.

Figure 3.8: A Hovered Bond

The bond is then defined as being hovered

Selecting Bonds

Bonds can only be selected when using the

selection tools discussed in Chapter 5. To

select bonds, first hover them and then press

the mouse down. The amber semicircles will

turn a blue color as shown in Figure 3.9.

Figure 3.9: A Selected Bond

Changing a Bond Type

To change a bond type, first select the bond

type you would like to change the bond to in

the Bonds toolbar. Then hover the bond with

the type that you would like to change and

click the mouse. The new bond type will

override the old type.

To change the bond types of a large number

of bonds to all be Single bonds, perform the

1. Select the bonds to be changed to Single

bonds using a selection tool as discussed

in Chapter 5.

77

2. Press the Saturate menu item in the

Structure menu.

Incrementing a Bond Order

When using the Single Bond tool, clicking on

hovered bonds will not override other bond

types. Instead the Single Bond tool will

increment the bond order. For example,

clicking on a Double bond will change it to a

Triple bond and clicking on the Triple bond

will change it to a Quadruple bond. Clicking

on a Sextuple bond will change the order

back to a Single bond.

This functionality can be disabled so that the

Single Bond tool overrides bond types in the

Deleting a Bond

To delete an bond, hover it and then press the

delete or backspace key. The constituent

atoms will remain.

Deleting Bonds Around Atoms

To delete bonds, but retain the atoms

contained in the bonds, perform the following

1. Select the bonds to be removed using a

selection tool as discussed in Chapter 5.

2. Press the Remove Selected Bonds menu

item in the Structure menu.

All selected bonds will be removed, but

atoms will remain present.

Changing the Z-Order of Bonds

When bonds overlap, one bond will be

rendered in front of the other. For structures

with 3D coordinates, the bond with the most

positive z-coordinates will be rendered on

top. Without z-coordinates, the last bond

drawn will be rendered on top.

To change the z-order of bonds when zcoordinates

are present, perform the

1. Select the structure with the z-orders to be

changed.

2. Select the Rotate in 3D tool in the

Content toolbar.

3. Click and drag the mouse to rotate the

structure in 3D so the desired bond is

placed on top.

4. Release the mouse to stop the rotation and

set the new coordinates.

are not present, perform the

1. Delete the bond that is to be rendered on

top.

2. Redraw the bond.

Chains

Chains are a group of carbon atoms, linked

linearly by bonds. Three types of chains are

provided in ChemDoodle:

• Carbon Chain - A consistent linear

carbon chain, with all chain angles

alternating at ±120° as shown in Figure

3.10.

Figure 3.10: A Carbon Chain

• Fisher Projection Chain - A straight

carbon chain, with all chain angles at 180°.

All non-terminal chain atoms also have two

additional carbon atoms depicted

78

perpendicular to the chain orientation as

shown in Figure 3.11.

Figure 3.11: A Fisher Projection Chain

• Random Chain - A carbon chain

where all chain angles are at 120°, but the

chain itself can deviate in any direction as

shown in Figure 3.12.

Figure 3.12: A Random Chain

Placing Chains at Fixed Angles

To place chains at fixed angles, perform the

1. Select a chain tool in the Shapes toolbar

using the Chain Tool group button.

2. Choose a starting atom to sprout the chain

from by hovering it. If you do not want to

start the chain from any existing atoms,

create an atom in a new place by clicking

on the Doodle Board where no atoms are

hovered.

3. Press the mouse down on the hovered

atom.

4. Drag the mouse to the desired length of

the chain. When using the Random chain,

drag the mouse in the outline of the chain

you would like to draw and the chain will

grow following that path.

5. Release the mouse to set the chain.

By default, the chains will be oriented at fixed

angles every 15° starting at 0°. All bond

lengths are defined by the Bond Length

visual specification in the Preferences

window under the Visuals tab under the

Bonds tab.

When dragging the mouse to define the chain,

a number will be displayed below the mouse

cursor to keep track of the number of bonds

being added.

Placing Chains at Non-fixed Angles

To place chains at non-fixed angles, hold

down the alt key while dragging the mouse

when defining the chain to break from the

fixed chain orientation angles.

Vertically and Horizontally

To place chains oriented vertically or

horizontally, hold down the shift key while

dragging the mouse when defining the chain.

The chain preview will then automatically

orient vertically or horizontally depending on

angle from the starting atom to the current

mouse cursor position.

Inverting Carbon Chains

Carbon chains can be inverted by holding

down the slash key (/) while placing. The

preview will update to reflect this.

Rings

Rings are a chain of carbon atoms where the

last atom in the chain connects to the first.

There may be bond types other than Single

bonds in rings. Currently the following rings

can be drawn quickly from the Rings toolbar,

with more ring choices in the Templates

widget:

• Cyclopropane ring

• Cyclobutane ring

79

• Cyclopentane ring

• Cyclohexane ring

• Cycloheptane ring

• Cyclooctane ring

• Cyclobutadiene ring

• Cyclopentadiene ring

• Benzene ring

• Cycloheptatriene ring

• Cyclohexane chair conformer 1

• Cyclohexane chair conformer 2

Placing a Ring

To place a ring, click the preferred ring tool in

in the Rings toolbar.

down. A preview of the new ring will be

drawn as shown in Figure 3.13.

Figure 3.13: New Ring Placement Preview

discussed in the following subsections to

place the ring in the preferred orientation.

Then release the mouse to set the ring.

The Optimize Zone can be used to optimize

ring placement as described in the Bonds

ring within these restraints, hover over an

Zone. The new ring placement will now

When placing rings outside of the Optimize

Placing Rings at Non-fixed Angles

80

Adding Rings to Bonds

When adding rings to atoms, you may not

always find it easy to achieve an aesthetic

fuse angle. To solve this, add the ring to a

bond instead of an atom. The ring will

automatically align to the bond it is being

added to.

To add rings to bonds, perform the following

1. Select a ring tool from the Rings toolbar.

2. Hover the bond a ring will be added to.

3. Click and drag the mouse pointer to the

side of the bond the ring should be added

to.

4. Release the mouse to set the ring.

When the mouse pointer is close to the bond

the ring is sprouting from, ChemDoodle will

automatically select the optimal side of the

bond to add to.

ChemDoodle contains a very advanced

structure templates system. Several sets of

predefined templates are already packaged

with ChemDoodle and can be accessed

through the Templates widget. Currently, the

following template sets are provided:

• Amino Acids

• Cycloalkanes

• Functional Groups

• Hexoses

• Nucleotides

• Polycyclic Aromatic Hydrocarbons

• Polycycles

• Ring Conformers

• Stereocenters and Geometries

Selecting a Template for Use

Just follow these three steps to select a

template for use:

Activate the Templates widget by clicking on

the Templates widget button.

1. Choose a template group from the drop

down selection.

2. Click on a template choice to choose a

template from the list.

3. Define a substitution atom by clicking on

the preferred atom in the main structure

panel. The substitution point will overlap

with the atom used as the growth position.

Placing templates is discussed in the

following subsections.

Placing a Template

To place a template, set up a template and

choose a substitution atom in the Templates

Then hover over the atom in the document

that you are attaching the template to and

81

press the mouse down. A preview of the

template will be depicted as in Figure 3.14.

Figure 3.14: New Template Placement Preview

place the template in the preferred orientation.

Then release the mouse to set the template.

template placement as described in the Bonds

section.

and Angles

template within these restraints, hover over an

orient towards the mouse pointed.

Preferences window under the General tab.

Lengths

When placing templates outside of the

Optimize Zone, fixed lengths will be

enforced. To break from fixed lengths, hold

down the shift key while placing the template.

Placing Templates at Non-fixed Angles

Optimize Zone, fixed angles will be

enforced. To break from fixed angles, hold

down the alt key while placing the template.

Lengths and Non-fixed Angles

Optimize Zone, fixed angles and fixed

lengths will be enforced. To break from fixed

lengths and fixed angles at the same time,

hold down both the shift and alt key while

placing the template.

Saving a New Template

To save a template into the Templates widget

library, perform the following steps:

1. Draw the desired template on the Doodle

Board.

2. Select the template with the selection

tools discussed in Chapter 5. Only a

82

single structure can be used in any

template.

3. Right-click after selecting the structure.

4. Press the Add Fragment as Template...

menu item to pop up the Add Template

5. Type in a name for the template in the

Template Name text field.

6. Choose a template group to add the

template to using the drop down selection.

You can create a new template group

using the Add Group button.

7. Click the Done button to add the

All of your templates are stored in the

templates folder in the ChemDoodleSettings

folder located in your operating system’s

standard Document folder. You may distribute

your template groups to other ChemDoodle

users or place third party template groups in

this folder to use them in ChemDoodle. If

ChemDoodle is open when manually placing

template groups in the templates folder, make

sure to first close and then restart

ChemDoodle for changes to take effect.

Managing your Templates

To manage your templates, click on the

Manage My Templates... menu item in the

Attributes

Attributes are special objects in ChemDoodle

that are associated with other chemical

objects. These include charges, radicals,

symbols and ids on atoms and ids on bonds.

They are both spatially and semantically

linked to the chemical object that they

describe. Any number of attributes can be

added to a single chemical object.

In addition to the standard attributes provided

in ChemDoodle, you can add your own text

based attributes as shown for the attribute

with display text of “attribute” for the

nitrogen atom as shown in Figure 3.15.

Figure 3.15: An Attribute on an Atom

Adding Attributes

To add a custom attribute, perform the

1. Hover the atom to add the attribute to.

2. Right-click on the hovered atom.

3. Press the Add Attribute... menu item.

4. Type in the text to be displayed in the

Display text field.

5. Type in an identifying name for the

attribute in the Name text field. This

value is used for the internal semantics

and is not rendered.

6. Press the Add button to set the attribute.

Hovering Attributes

You can hover attributes by using any of the

selection tools. First, make sure the current

selection is empty and then move the mouse

cursor close to the center of the attribute so

that it is closer to the attribute than any other

chemical objects. The attribute will then be

defined as hovered and an amber circle will

be rendered on top of it as shown in Figure

3.16.

Figure 3.16: A Hovered Attribute

83

To help identify which object the attribute

describes, a transparent amber circle is drawn

over that object (the nitrogen atom in Figure

3.16).

Selecting Attributes

Attributes can only be selected when using

the selection tools discussed in Chapter 5. To

select attributes, first hover them and then

turn a blue color as shown in Figure 3.17.

Figure 3.17: A Selected Attribute

Editing Attributes

The display text and names of custom

attributes can be edited at any time by

performing the following steps:

1. Hover the attribute to be edited.

2. Right-click on the hovered attribute.

3. Press the Format Attribute... menu item.

4. In the visual specifications window that

appears, change the Name and Display

text to the new values.

5. Click the Done button to set the new text

values.

Moving Attributes

To move attributes, perform the following

1. Hover the attribute to be moved.

2. Press the mouse down to select the

hovered attribute.

3. Drag the attribute to the new preferred

location.

4. Release the mouse to set the new position.

Attributes can only be moved a certain

distance from the object that they describe.

This distance is specified by the Allow

Distance visual specification in the

under the Attributes tab. Change this to suit

your needs.

Removing Attributes

To remove an attribute, use the Eraser tool

and to click on the hovered symbol or hover

the symbol with the selection tools and press

the delete or backspace key.

Charges

Charges are attributes can be associated with

any atoms as shown in Figure 3.18. Both

positive and negative values can be used.

Figure 3.18: A Charge Attribute

84

Adding Charges

To add charge to an atom, perform the

1. Select the Increase Charge or

Decrease Charge tools in the

Attributes group button in the Shapes

toolbar.

2. Hover the atom to add charge to.

3. Press the mouse down to add the charge.

4. If you prefer to have the charge placed

elsewhere, then before releasing the

mouse, drag the pointer to the desired

5. Release the mouse to set the charge.

To change the charge of an atom, perform the

2. Hover the atom to with the charge to be

3. Click the mouse down to increment or

decrement the charge.

The + and - keys on the keyboard can also be

used to increment and decrement charge

Removing Charges

Removing charges can be done is several

• Decrement or increment the charge value to

0 using the Increase Charge and Decrease

Charge tools.

• Select the Eraser tool and click on a

hovered charge to remove it.

• Hover the charge using the selection tools

and press the delete or backspace key.

Radicals

Radical types can be associated with any

atoms as shown in Figure 3.19. Currently

only Monovalent and Divalent Singlet types

are supported.

Figure 3.19: A Radical Attribute

Adding Radicals

To add a radical electron to an atom, perform

the following steps:

1. Select the Increase Number of Radical

Electrons tool in the Attributes

group button in the Shapes toolbar.

2. Hover the atom to add the radical to.

3. Press the mouse down to add the radical.

4. If you prefer to have the radical placed

5. Release the mouse to set the radical.

Number of Radical Electrons

Electrons or Decrease Number of

85

Radical Electrons tools in the

2. Hover the atom with the radical to be

decrement the the number of radical

electrons.

Removing Radicals

Removing radicals can be done is several

ways:

• Decrement the radical value to 0 using the

Decrease Number of Radical Electrons

hovered radical to remove it.

• Hover the radical using the selection tools

Symbols are standard types of atom

decorations that can be associated with any

atoms such as the Radical Cation symbol

shown in Figure 3.20.

Figure 3.20: A Symbol Attribute

Currently, included symbols are:

1. Single Electron

2. Electron Pair aka. Non-bonding Pair,

Lone Pair

3. Radical Cation

4. Radical Anion

5. Electron Pair (Bar)

6. Positive Dipole

7. Negative Dipole

Adding Symbols

To add a symbol to an atom, perform the

1. Select the desired symbol tool in the

2. Hover the atom the symbol will added to.

3. Press the mouse down to add the symbol.

4. If you prefer to have the symbol placed

5. Release the mouse to set the symbol.

Removing Symbols

To remove a symbol, use the Eraser tool and

to click on the hovered symbol or hover the

symbol with the selection tools and press the

delete or backspace key.

Isotopes

Mass numbers can be associated with atoms

with element symbols as their label to

designate isotopes. All mass numbers are

displayed in superscript format to the left of

element symbols as shown in Figure 3.21.

Figure 3.21: A Carbon-13 Isotope

If you later change an atom’s label and there

is a mass number associated with that atom,

then the mass number will be removed.

Numbers

To set a published mass number to an element

atom, perform the following steps:

86

1. Hover the atom with the mass number to

be set.

3. Expand the Mass Number submenu.

4. Press any of the listed values to set the

mass number of the isotope.

To set an arbitrary mass number to an element

4. Press the Other... menu item.

5. Type in an integer value into the text field

that appears.

6. Click the Accept button to set the mass

number.

Removing Mass Numbers

To remove a mass number from an atom:

be removed.

4. Press the Remove Mass Number menu

item to remove the mass number.

Orbitals

2D graphics for various orbital shapes can be

placed directly into the document or attached

onto structures. Use them to show more

detailed chemical figures. Each orbital shape

has several different shading and fill styles.

The following orbital types are provided:

• Atomic s Orbitals

• Atomic px|y|z Orbitals

• Atomic dxz|yz|xy|x 2 -y 2 Orbitals

• Atomic dz 2 Orbitals

• Atomic fxz 2 |xy 2 |x(x 2 -3y 2 )|y(3x 2 -y 2 ) Orbitals

• Atomic fz 3 Orbitals

• Hybrid sp 3 Orbitals

• Hybrid sp Lobes

• Bonding σ Orbitals

• Bonding π Orbitals

Orbitals are defined by two anchor points as

shown in Figure 3.22. The first anchor point

defines the center of the orbital while the

second anchor point defines the extent of the

orbital.

Figure 3.22: Orbital and Anchors

87

To place an orbital, perform the following

1. Select an orbital tool by expanding any of

the Orbital group button in the Orbitals

2. Press the mouse down on the Doodle

Board to set the center of the orbital.

3. Drag the mouse to preview the placement

of the extent of the orbital. A dotted green

outline of the orbital will be shown.

4. Release the mouse to set the orbital.

You can also click the mouse to set the start

center then move the mouse and click again

to set the extent.

In step 2, you may want to attach the orbital

to an atom or bond center. ChemDoodle will

automatically lock onto atoms and bonds

when placing orbitals if the mouse pointer

gets close enough to them. Once the atom or

bond has been highlighted, continue through

step two to place the orbital and set the center

to be the atom or bond center.

or Angles

To place lines at non-fixed lengths or angles,

hold down the alt key while dragging the

mouse when defining the orbital to break

from the fixed lengths and angle orientations.

Forcing Orbitals to be Drawn Vertically

and Horizontally

To place orbitals oriented vertically or

dragging the mouse when defining the orbital.

The orbital preview will then automatically

the angle from the start point to the current

Moving Orbitals

To move orbitals, use a selection tool, either

the lasso or the rectangular marquee. Make

emptying the current selection. Perform the

1. Hover the mouse pointer over the orbital

so an open hand mouse cursor appears

and the rectangle anchor points are drawn

as shown in Figure 3.19.

2. Press the mouse down and drag to move

the orbital.

3. Release the mouse to finish the move

Resizing Orbitals

To resize orbitals, use a selection tool, either

and the orbital anchor points are drawn as

shown in Figure 3.19.

88

2. Move the mouse pointer over one of the

two end anchor points so that anchor point

is filled in with an amber color.

3. Press the mouse down so the anchor point

is filled with a blue color.

4. Drag the anchor point to resize the orbital.

5. Release the mouse to finish the resize

Removing Orbitals

Orbitals can be removed in a number of ways.

You can do the following:

• Use a selection tool to hover the mouse

pointer over the orbital so an open hand

mouse cursor appears and the rectangle

anchor points are drawn as shown in Figure

3.19. Then press the backspace or delete

key.

• Use the eraser tool to hover the mouse

pointer over the orbital so the orbital anchor

points are drawn. Then click with the

In addition to chemical structures,

ChemDoodle provides tools for drawing

shapes for advanced figures.

This section introduces the new user to shapes

within ChemDoodle. It covers the following

topics:

• The different types of shapes.

• How to draw shapes.

• Adding arrows to figures.

• Adding text to figures.

• How to move shapes.

• How to resize shapes.

• How to remove shapes.

• What the anchor decorations mean.

Anchors

Anchors are points that define a given shape.

By moving them, you modify how the shape

appears. There are two types of anchors,

control anchors and corner/edge anchors.

Control Anchors

Control anchors represent points that can be

moved anywhere and have no relationship to

other anchors, such as in lines, custom shapes

or orbitals. They appear as compass shapes as

shown in Figure 4.1.

Figure 4.1: Control anchors

89

Corner/Edge Anchors

Corner edge anchors define corners and edges

of shapes. Moving these anchors will change

the shape in relationship to the other anchors.

For instance, if you move a left-right pointing

anchor, you will not affect the vertical

positioning of the other anchors. These

anchors are present for box shaped objects,

like rectangles and ovals. They appear as

double sided arrows as shown in Figure 4.2.

Figure 4.2: Corner/Edge Anchors

Lines

Lines are the most basic shape and are

defined by two anchors placed at their

endpoints as shown in Figure 4.3. There is

also a third anchor at the midpoint for

controlling the arc angle. This anchor point is

discussed in the next section (Arcs).

Figure 4.3: Line Shape and Anchors

Drawing Lines at Fixed Angles

To draw a line at fixed angles, perform the

following steps:

1. Select a line tool by expanding the Lines

Board to set the start point of the line.

of the end of the line.

4. Release the mouse to set the line.

point then move the mouse and click again to

set the end point.

By default, lines will be oriented at fixed

angles every 15° starting at 0°.

Drawing Lines at Non-fixed Angles

To place lines at non-fixed angles, hold down

the alt key while dragging the mouse when

defining the line to break from the fixed

orientation angles.

To place lines oriented vertically or

dragging the mouse when defining the line.

The line preview will then automatically

Moving Lines

To move lines, use a selection tool, either the

lasso or the rectangular marquee. Make sure

that no content is currently selected by

1. Hover the mouse pointer over the line so

an open hand mouse cursor appears and

the anchor points are drawn as shown in

Figure 4.3.

the line.

90

Resizing Lines

To resize lines, use a selection tool, either the

the line anchor points are drawn as shown

in Figure 4.3.

4. Drag the anchor point to resize the line.

Removing Lines

Lines can be removed in a number of ways.

pointer over the line so an open hand mouse

cursor appears and the line anchor points

are drawn as shown in Figure 4.3. Then

press the backspace or delete key.

pointer over the line so the line anchor

mouse.

Arcs

Arcs are segments of a circle and are defined

by two anchors placed at their endpoints as

shown in Figure 4.4. There is also a third

anchor at the middle for controlling the arc

angle. Only 90°, 120°, 180° and 270° arcs are

directly provided in the Arcs group button,

but an arc of any angle can be drawn. The

only difference between the line shape and

the arc shape is the angle, and either shape

can be converted into the other by changing

this value.

Figure 4.4: Arc Shape and Anchors

Drawing Arcs at Fixed Angles

To draw an arc at fixed angles, perform the

1. Select an arc tool by expanding the Arcs

Board to set the start point of the arc.

of the end of the arc.

4. Release the mouse to set the arc.

By default, arcs will be oriented at fixed

Drawing Arcs at Non-fixed Angles

To place arcs at non-fixed angles, hold down

defining the arc to break from the fixed

To place arcs oriented vertically or

91

dragging the mouse when defining the arc.

The arc preview will then automatically

Moving Arcs

To move arcs, use a selection tool, either the

1. Hover the mouse pointer over the arc so

the arc anchor points are drawn as shown

in Figure 4.4.

the arc.

Resizing Arcs

To resize arcs, use a selection tool, either the

4. Drag the anchor point to resize the arc.

Changing Arc Angles

Arc angles can be changed using the midpoint

anchor. Choose a selection tool, either the

2. Move the mouse pointer over the middle

anchor point so that it is filled in with an

amber color.

4. Drag the anchor point to change the arc

angle.

5. Release the mouse to set the new arc

While changing the angle of arcs, the arc

angle will be displayed below the mouse

cursor.

Flipping an Arcʼs Orientation

To flip an arc’s orientation, so that the curve

faces the opposite direction. use a selection

tool, either the lasso or the rectangular

marquee. Make sure that no content is

currently selected by emptying the current

selection. Perform the following steps:

2. Right-click on the hovered arc.

3. Select the Flip Arc menu item to flip the

arc’s orientation.

92

You can also click and drag the midpoint to

the other side of the arc to perform this task.

Removing Arcs

Arcs can be removed in a number of ways.

pointer over the arc so an open hand mouse

cursor appears and the arc anchor points are

drawn as shown in Figure 4.4. Then press

the backspace or delete key.

pointer over the arc so the arc anchor points

are drawn. Then click with the mouse.

Arrows

Arrows are essential in chemical graphics for

many reasons, the most important being for

reaction and mechanism diagrams. Arrows

are so important that they have their own

unique toolbar. Essentially, arrow shapes are

just lines and arcs with arrowheads as shown

in Figure 4.5.

Figure 4.5: Arrow Shape and Anchors

ChemDoodle also provides advanced features

for building and defining reactions. Reactions

are covered in Chapter 7.

Drawing Arrows at Fixed Angles

To draw an arrow at fixed angles, perform the

1. Select the desired arrowheads and

connector styles in the Arrows toolbar.

2. Click on one of the arc angle buttons in

the Arrows toolbar to enter the arrow

placement mode.

3. Press the mouse down on the Doodle

Board to set the start point of the arrow.

4. Drag the mouse to preview the placement

of the end of the arrow.

5. Release the mouse to set the arrow.

By default, arrows will be oriented at fixed

To place arrows at non-fixed angles, hold

when defining the arrow to break from the

fixed orientation angles.

To place arrows oriented vertically or

dragging the mouse when defining the arrow.

The arrow preview will then automatically

Moving Arrows

To move arrows, use a selection tool, either

1. Hover the mouse pointer over the arrow

and the arrow anchor points are drawn as

shown in Figure 4.5.

the arrow.

93

Resizing Arrows

To resize arrows, use a selection tool, either

4. Drag the anchor point to resize the arrow.

Changing Arrow Arc Angles

Arrow arc angles can be changed using the

midpoint anchor. Choose a selection tool,

either the lasso or the rectangular marquee.

Make sure that no content is currently

selected by emptying the current selection.

Perform the following steps:

anchor point so that anchor point is filled

in with an amber color.

4. Drag the anchor point to change the arrow

5. Release the mouse to set the new arrow

arc angle.

While changing the angle of arrow arcs, the

arrow arc angle will be displayed below the

mouse cursor.

NOTE: A few special arrow types, such as

the retrosynthetic type, are straight, and

you will not be able to change the arc

angles for these types.

Removing Arrows

Arrows can be removed in a number of ways.

pointer over the arrow so an open hand

mouse cursor appears and the arrow anchor

points are drawn as shown in Figure 4.5.

Then press the backspace or delete key.

pointer over the arrow so the arrow anchor

Editing Arrowheads

Arrowheads can be added/removed from the

ends of the line shape. This can be done

before they are drawn, with the Arrow

toolbar, or afterwards by using the Format

Arrow window.

There are several settings that control how

arrowheads are drawn:

• Indented - When selected, the back end of

the arrow will be indented in.

• Filled - When selected, the arrow will be

filled in, otherwise it will just be an outline.

• Chevroned - When selected, the arrow will

be drawn as a simple chevron.

• Length - This setting controls the length of

the arrow head along the line.

94

• Angle - This setting controls the angle of

the arrow, from one side to the other.

Use these settings to control how arrowheads

are drawn.

NOTE: If the arrowhead length is greater

than 50% of the length of the line it is on,

then the length will be decreased to 50% of

the length of the line it is on.

Rectangles

Rectangles can be drawn in several styles and

are defined by two anchor points that

correspond to a pair of rectangle corners

along one of the diagonals as shown in Figure

4.6.

Figure 4.6: Rectangle Shape and Anchors

Drawing Rectangles

To draw a rectangle, perform the following

1. Select a rectangle tool by expanding the

Rectangle group button in the Shapes

Board to set one corner of the rectangle.

of the opposite corner along the diagonal

of the rectangle.

4. Release the mouse to set the rectangle.

set the end point.

Drawing Squares

To draw squares, hold down the shift key

while dragging the mouse when defining the

rectangle to force the width and height to be

equivalent.

Moving Rectangles

To move rectangles, use a selection tool,

1. Hover the mouse pointer over the

rectangle so an open hand mouse cursor

appears and the rectangle anchor points

are drawn as shown in Figure 4.6.

the rectangle.

Resizing Rectangles

To resize rectangles, use a selection tool,

anchor points so that anchor point is filled

4. Drag the anchor point to resize the

rectangle.

95

Non-rounded Rectangles

To change a rectangle into a roundedrectangle

or vice versa, use a selection tool,

appears and the arrow anchor points are

drawn as shown in Figure 4.6.

2. Right-click on the hovered rectangle and

select the Format Rectangle... menu

item.

3. Scroll to the Rectangle section and use

the Rounded on/off choice to set the

rectangle to be rounded or not.

Removing Rectangles

Rectangles can be removed in a number of

ways. You can do the following:

pointer over the rectangle so an open hand

4.4. Then press the backspace or delete key.

pointer over the rectangle so the rectangle

anchor points are drawn. Then click with

the mouse.

Ovals

Ovals can be drawn in several styles and are

defined by two anchor points that correspond

to a pair of rectangle corners along one of the

diagonals that circumscribes the oval as

shown in Figure 4.7.

Figure 4.7: Oval Shape and Anchors

Drawing Ovals

To draw an oval, perform the following steps:

1. Select an oval tool by expanding the Oval

Board to set one corner of the

circumscribing rectangle.

of the circumscribing rectangle.

4. Release the mouse to set the oval.

Drawing Circles

To draw circles, hold down the shift key while

dragging the mouse when defining the oval to

force the major and minor axes lengths to be

Moving Ovals

To move ovals, use a selection tool, either the

1. Hover the mouse pointer over the oval so

the oval anchor points are drawn as shown

in Figure 4.7.

the oval.

96

Resizing Ovals

To resize ovals, use a selection tool, either the

4. Drag the anchor point to resize the oval.

Removing Ovals

Ovals can be removed in a number of ways.

pointer over the oval so an open hand

mouse cursor appears and the oval anchor

points are drawn as shown in Figure 4.7.

pointer over the oval so the oval anchor

Brackets

Brackets can be drawn in several styles and

correspond to a pair of rectangle corners

along one of the diagonals that defines the

bracket space as shown in Figure 4.8.

Figure 4.8: Bracket Shape and Anchors

There are currently 4 bracket styles:

• Square Brackets - [ ]

• Parenthesis - ( )

• Curly Brackets - { }

• Chevrons - < >

Drawing Brackets

To draw a set of brackets, perform the

1. Select a bracket tool by expanding the

Bracket group button in the Shapes

Board to set one corner of the bracket.

of the bracket.

4. Release the mouse to set the bracket.

and Height

To draw square brackets, hold down the shift

key while dragging the mouse when defining

the bracket to force the width and height of

the bracket content to be equivalent.

97

Moving Brackets

To move brackets, use a selection tool, either

1. Hover the mouse pointer over the brackets

and the bracket anchor points are drawn

as shown in Figure 4.8.

the brackets.

Resizing Brackets

To resize brackets, use a selection tool, either

4. Drag the anchor point to resize the bracket

set.

Editing Bracket Lip Protrusion

To change the widths of the current bracket

rendering style, use a selection tool, either the

that no content is currently selected by

shown in Figure 4.8.

select the Format Bracket... menu item.

3. Scroll to the Bracket section and use the

Wideness number slider to define how

protruded bracket lips are rendered.

Removing Brackets

Brackets can be removed in a number of

pointer over the brackets so an open hand

mouse cursor appears and the bracket

4.8. Then press the backspace or delete key.

pointer over the brackets so the bracket

Custom Shapes

In addition to the standard defined shapes

previously discussed, ChemDoodle allows

you to create custom shapes. Currently there

are three types of custom shapes:

• Pen - The Pen tool allows you to draw

any shape by clicking and dragging an

outline.

• Bezier Curve - The Bezier Curve tool

allows you to draw a bezier curve by

defining its control points.

98

• Polyline - The Polyline tool allows you

do draw any polygon shape that can be

convex or concave.

Both pen paths and polylines can be open or

closed and are defined by their control points,

which the shape will pass through as shown

in Figure 4.9.

Figure 4.9: Pen and Polyline Control Points

Bezier curves can be open or closed and are

defined by a more complex set of control

points as shown in Figure 4.10.

Figure 4.10: Bezier Control Points

Drawing with the Pen Tool

To draw a custom shape with the Pen tool,

1. Select a Pen tool by expanding the

Custom Shapes group button in the

Shapes toolbar.

Board to begin drawing.

3. Drag the mouse in an outline of the shape

you would like.

4. Release the mouse to set shape.

ChemDoodle will automatically simplify your

path for you and generate a cubic

interpolation.

Drawing with the Polyline Tool

To draw a custom shape with the Polyline

tool, perform the following steps:

1. Select the Polyline tool by expanding the

Board to set the first point.

3. Move the mouse to location you prefer the

next point to be placed.

4. Click to place the next point. Points will

automatically connect to previous points.

5. Repeat steps 3 and 4 until finished.

6. Click on the first point drawn or doubleclick

the last point to complete the shape

and set it.

Moving Pen Paths and Polylines

To move custom shapes, use a selection tool,

1. Hover the mouse pointer over the custom

shape so an open hand mouse cursor

appears and the control points are

rendered as shown in Figure 4.9.

the custom shape.

99

Modifying Pen Paths and Polylines

You can move the control points that define

pen paths and polylines. To do so, use a

selection tool, either the lasso or the

rectangular marquee. Make sure that no

content is currently selected by emptying the

current selection. Perform the following

appears and the control points are drawn

as shown in Figure 4.9.

control points that you desire to be moved

so that control point is filled in with an

3. Press the mouse down so the control point

4. Drag the control point to move it.

5. Release the mouse to finish.

Drawing with the Bezier Tool

Bezier curves are defined by pairs of control

points. There is a main point which the curve

passes through, and a second control point

that describes the tangent of the line at the

point that the curve passes through. To draw a

bezier curve, perform the following steps:

1. Select the Bezier Curve tool by

expanding the Custom Shapes group

button in the Shapes toolbar.

3. Drag your mouse to set the paired control

point that defines the tangent of the curve

at the first point. The further from the first

point you make this paired control point,

the tighter the curve will hug the first

4. Release the mouse to set the paired

control point.

5. Move the mouse to location you prefer the

next point to be placed that the curve will

pass through.

6. Press the mouse down to place the next

point. Points will automatically connect to

previous points.

7. Drag your mouse to set the paired control

at the second point. The further from the

second point you make this paired control

point, the tighter the curve will hug the

second point.

8. Repeat steps 5 through 7 until finished.

9. Press the escape key to complete the

shape and set it.

Modifying Bezier Curves

bezier curves in one of two ways. The first

way is by following the same instructions as

in the Modifying Pen Paths and Polylines

section. The second is by using the Bezier

Curve tool. Perform the following steps:

2. Move the mouse pointer over the bezier

curve that you desire to be modified so

that its control points are rendered.

3. Click on the bezier curve so that all of its

control points are rendered as shown in

Figure 4.10.

4. Hover over any of the control points so

that an amber color fills the one you wish

to move.

100

5. Press the mouse down and drag the

control point to the new desired location.

6. Release the mouse to finish moving the

Deleting Bezier Control Points

Only the control points that have the curve

pass through them may be deleted. Deleting

one of these control points will also remove

the corresponding paired control point. To

delete a bezier control point, perform the

4. Hover over the control point that you wish

to remove so that it is filled in with an

5. Press the delete key to delete the control

point.

Adding Arrows to Bezier Curves

To add arrows to bezier curves follow the

same procedures as discussed for the Arrow

shapes earlier in the Chapter. Just right click

on the bezier curve after it is hovered, select

the Format Bezier Curve... menu item, and

define the arrow sections to your preference.

To close or open a custom shape, use a

content is currently selected by emptying the

drawn as shown in Figure 4.9.

2. Right-click on the hovered custom shape

and select the Format Custom Shape...

menu item.

3. Scroll to the Path or Bezier Curve

section and use the Close on/off choice to

set if the custom shape path is closed or

not.

If closed, the custom shape can be filled in

with a desired color.

Removing Custom Shapes

Custom Shapes can be removed in a number

of ways. You can do the following:

pointer over the custom shape so an open

hand mouse cursor appears and the custom

shape anchor points are drawn as shown in

Figure 4.9. Then press the backspace or

delete key.

pointer over the custom shape so the custom

shape anchor points are drawn. Then click

with the mouse.

Rulers

Rulers measure distances in 2 dimensions and

are defined by two anchors placed at their

endpoints as shown in Figure 4.11. There is

also a third midpoint in the middle for

discussed in the next section.

Figure 4.11: Ruler Shape and Anchors

101

Drawing Rulers at Fixed Angles

To draw a ruler at fixed angles, perform the

1. Select a Ruler tool in the Shapes toolbar.

Board to set the start point of the ruler.

of the end of the ruler.

4. Release the mouse to set the ruler.

By default, rulers will be oriented at fixed

To place rulers at non-fixed angles, hold

when defining the ruler to break from the

To place rulers oriented vertically or

dragging the mouse when defining the ruler.

The ruler preview will then automatically

angle from the start point to the current

Automatically Measuring Object Width

To measure the width and height of selected

objects, perform the following procedure:

1. Select the content to be measured using

the selection tools.

2. Select the Width and Height menu item

in the Measure> submenu in the Content

menu.

Two rulers will be placed to measure the

width and height of the selected content.

Diagonal

To measure the diagonal of selected objects,

perform the following procedure:

2. Select the Diagonal menu item in the

Measure> submenu in the Content

A single ruler will be placed across the

diagonal of the selected content.

Moving Rulers

To move rulers, use a selection tool, either the

1. Hover the mouse pointer over the ruler so

Figure 4.11.

the ruler.

Resizing Rulers

To resize rulers, use a selection tool, either

102

the ruler anchor points are drawn as

shown in Figure 4.11.

4. Drag the anchor point to resize the ruler.

Ticks

To show and hide ruler major and minor ticks,

use a selection tool, either the lasso or the

2. Right-click on the hovered ruler and

select the Format Ruler... menu item.

3. Scroll to the Ruler section and use the

Show Major Ticks and Show Minor

Ticks on/off choices to set whether major

and minor ticks are visible or not.

Changing the Measurement Unit

To change the ruler’s measurement unit, use a

Unit drop down selection to select the

unit to be displayed.

Removing Rulers

Rulers can be removed in a number of ways.

pointer over the ruler so an open hand

mouse cursor appears and the ruler anchor

points are drawn as shown in Figure 4.11.

pointer over the ruler so the ruler anchor

Text Areas

In addition to atom labels, you can also add

blocks of text in text area objects. Text areas

can have a border and can have a background,

and can be resized to any dimension.

To place text areas, click on the Text Area

tool in the Shapes toolbar. You can place

text areas and edit them just as you would

Rectangle shapes. The text area is resizable

and can have a border and background. It will

not automatically fit its contained text.

103

When editing the text area, text format

functions will be provided in a toolbar that

appears above it as shown in Figure 4.12.

Figure 4.12: Editing a Text Area

To edit text areas, use the Text Area tool to

click on an existing text area, or hover the

text area using a selection tool and doubleclick.

Chapter 5: Editing

The most important feature of graphical

editors is access to a robust set of content

management tools.

content management tools within

• Selecting content.

• Duplicating content.

• Editing content.

• Organizing content.

• Grouping content.

• Removing content.

Selecting Content

Content can be selected by using any of the

selection tools. There are 3 types of selection

tools provided in ChemDoodle:

• Lasso - Define an arbitrary boundary

that follows the mouse and selects any

objects contained within.

• Rectangular Marquee - Define a

rectangle that selects any objects contained

within.

• Lasso Only Shapes - Define an

arbitrary boundary that follows the mouse

and selects only shape objects contained

104

These tools can be quite complex to learn, so

we suggest you practice with them for a

while.

Selected content will show an amber

highlight and will be surrounded by an an

animated amber outline as shown in Figure

5.1.

Figure 5.1: Selected Content

The crawling ants animation can be turned off

in the Preferences window under the

Selecting Individual Objects

To select an individual object, first select a

lasso tool and make sure no content is

currently selected. Then hover the object to

be selected and click. The single object will

then be selected.

Selecting Groups of Objects

To select groups of object, perform the

1. Select a lasso tool.

2. Click and drag to draw an outline with a

lasso or to draw a rectangle with the

rectangular marquee to surround all of the

objects you would like to select.

3. Release the mouse to select the contained

NOTE: It may be difficult to see the full

bounds for some shapes, such as large text

areas with little text in them. If you have

trouble selecting a shape, make sure to

discover where its bounds are and draw the

selection bounds around both anchors.

Select All

To select all content on a page, expand the

Select submenu in the Content menu and

press the All menu item. The keyboard

shortcut to use this function is ctrl-A

(command-A on Mac OS X).

from a Selection

If a selection has already been made, you can

add or remove an individual object from the

selection. Hold down the alt key and hover

the object to be added or removed and click

the mouse. If that object was previously

selected, it will be removed from the

selection, otherwise it will be added to the

selection.

add or remove groups of objects from the

selection. Hold down the shift key and hover

and drag to draw an outline with a lasso or to

draw a rectangle with the rectangular

marquee to surround all of the objects you

would like to select or deselect. Then release

the mouse. Any objects contained within the

new boundary will be removed from the

selection if they were previously selected,

otherwise they will be added to the selection.

Selecting Whole Molecules

Instead of surrounding an entire molecule

with the selection tools to select it, the

following techniques will allow you to select

individual molecules:

105

• Using a selection tool, hold down both the

alt and shift keys and then click on an atom

or bond in the molecule.

• Press the tab key to navigate through

molecules, selecting one at a time, starting

at the last drawn molecule and then

navigating through them chronologically.

SMARTS

SMARTS is single line, text-based query

system for matching chemical objects, similar

to how systems like regular expressions

match text. You may find it very convenient

to select content in files by SMARTS queries.

To do so, perform the following steps:

1. Select the SMARTS... menu item in the

Select> submenu in the Content menu.

2. A window will appear prompting you for

the SMARTS query. Input your query

here and press the Accept button.

Any content that matches the SMARTS string

will then be selected.

Navigating Through Single Shapes

Instead of surrounding an entire shape with

the selection tools to select it or clicking on

the shape, you can also press the tab key

while holding down the shift key to navigate

through shapes, selecting one at a time,

starting at the last drawn shape and then

Selecting Only Shapes

When figures are highly congested, it may be

difficult to select shapes from surrounding

structures. In this case, use the Lasso Only

Shapes tool which will only recognize

shapes. The Lasso Only Shapes tool works

identically to the Lasso tool in every other

Selection

To select the inverse of the current selection

on a page, expand the Select submenu in the

Content menu and press the Inverse menu

Deselecting Objects

To deselect the current selection, perform one

of the following actions:

• Move the mouse cursor away from the

selection so that the lasso cursor icon

appears. Then click the mouse.

• When the mouse cursor is within the current

selection boundary, double-click the mouse.

• Press the Deselect menu item in the

Content menu.

• Press the space key to deselect the current

selection and return to the structure drawing

mode.

Reselecting Objects

If you lost the current selection by mistake,

you can reselect it by selecting the Reselect

menu item in the Content menu.

Duplicating Content

Content in ChemDoodle can be duplicated on

the Doodle Board in the current document or

between separate documents through copy

and paste actions. To have ChemDoodle

objects copied and pasted correctly on the

Doodle Board, make sure to keep

ChemDoodle Collage enabled in the

Preferences window under the Advanced

Copy and Paste

To duplicate content, perform the following

1. Select the content to be duplicated.

106

2. Press the Copy menu item in the Edit

menu. The keyboard shortcut to use this

function is ctrl-C (command-C on Mac

OS X).

3. Press the Paste menu item in the Edit

function is ctrl-V (command-V on Mac

Cut and Paste

To duplicate content and remove the original,

2. Press the Cut menu item in the Edit

function is ctrl-X (command-X on Mac

Organizing Content

ChemDoodle provides several tools for laying

out content in the document.

Aligning

To align content relative to each other,

1. Select the content to be aligned.

2. Expand the Align submenu in the

Content menu and press the Left Edges,

Horizontal Centers, Right Edges, Top

Edges, Vertical Centers or Bottom

Edges menu items.

Aligning by Bond

To align an entire molecule by a given bond,

1. Hover the bond to align the molecule by.

2. Press the up, down, left or right arrow

keys to align the bond from its first to

second constituent atom in the selected

direction. This will rotate the entire

molecule with the bond.

Centering

To center all content on the page, expand the

Center submenu in the Content menu and

press the All on Page menu item.

To center selected content on the page,

1. Select the content to be centered.

2. Expand the Center submenu in the

Content menu and press the Selection on

Page, Selection Horizontally or

Selection Vertically menu items.

Distributing

To distribute content across the document,

1. Select the content to be distributed.

2. Expand the Distribute submenu in the

Content menu and press the Horizontally

on Page or Vertically on Page menu

items.

To distribute content across the document

using a buffer spacing that you provide,

by Buffer Space... or Vertically by

Buffer Space... menu items.

3. Input a buffer space value into the number

field that appears.

4. Click the Accept button to perform the

distribution.

107

Flipping

To flip content horizontally or vertically,

1. Select the content to be flipped.

2. Expand the Flip submenu in the Content

menu and press the Horizontally or

Vertically menu items.

Flipping a Bond

You may wish to flip non-symmetrical bonds

when you need it to face the other direction,

such as when working with wedge bonds.

There are a few quick ways to do so:

• Hover over the bond and press the f key to

flip it.

• Hover the bond, right-click and select Flip

Bond Orientation.

• Use the bond tool of that bond type and

click on the bond after hovering it.

ChemDoodle will detect the bond is being

set to its current bond type and will instead

flip the bond.

Placing in Grid

To place all content in a grid that covers the

document, perform the following steps:

1. Select the Grid All on Page... submenu in

the Content menu.

2. In the prompt that appears, select whether

you want to specify the grid dimensions

by Columns or by Rows by choosing the

corresponding selection from the drop

down menu.

3. Input the dimension of the grid in the

number field. The other dimension will be

automatically calculated based on the

number of objects being placed in the

grid.

4. Select the Grid button.

Stacking

Stacking will place all content on the page

starting from the top-left of the document to

the bottom-right, such that their visual bounds

are separated by a small buffer and that all

objects are within the page margins. To stack

all content on the page, press the Stack All on

Page menu item in the Content menu.

If content is ever placed outside of the page

bounds, red strips will appear at the sides of

the page that the content extends from. Click

on the red strip to stack all of the content that

extends from that side of the page back onto

the page.

Framing Content

Content can be automatically framed with

various different shapes. To frame objects,

1. Select the objects to be framed using the

selection tools.

2. Expand the Add Frame> submenu in the

3. Select the type of frame to use.

The selected content will then be framed.

Editing Content

The selection area is context sensitive and

you can click and drag on the various features

of the selection to perform different actions.

Translating

To translate content, or move it on the page,

1. Select the content to be translated.

2. Hover the mouse cursor over the selection

so that an open hand cursor appears.

108

3. Press the mouse down so the mouse

cursor turns into a closed hand cursor.

4. Drag the mouse to translate the content.

5. Release the mouse to finish the

translation.

During the translation, the change in x

position and change and y position will be

displayed below the mouse cursor. You can

disable this feedback in the Preferences

window under the General tab.

If you hold the shift key down while

translating will lock the content horizontally

or vertically depending on where the mouse

pointer is.

If you hold the shift and alt keys down while

translating content, you will duplicate that

content and it will be locked horizontally or

vertically depending on where the mouse

pointer is. To remove the lock, release the

shift and alt keys.

Rotating

To rotate content, perform the following

1. Select the content to be rotated.

2. Hover the mouse just outside the edge of

the selection border so that the rotation

cursor appears.

3. Press the mouse down and drag it to rotate

the content.

4. Release the mouse to finish the rotation.

During the rotation, the rotation angle will be

window under the General tab.

To more precisely rotate content, perform the

2. Expand the Rotate submenu in the

Content menu and press the 90° CW, 90°

CCW or 180° menu items.

To more precisely rotate content by an

arbitrary angle, perform the following steps:

Content menu and press the Arbitrary...

3. Enter a degree value in the number field

that appears and select whether the

rotation should be done clockwise or

counterclockwise.

4. Press the Rotate button to perform the

rotation to the settings you provided.

Moving the Rotation Anchor

Sometimes you may not want to rotate

content around its center, as is done by

default. For instance, you may desire to rotate

structures around an atom. This can be

achieved by moving the rotation anchor that

is initially found in the center of the selection.

To move the rotation anchor, perform the

1. Move the mouse over the rotation anchor

so that the anchor fills in with an amber

color and the mouse cursor changes to a

resize cursor.

2. Press the mouse down and drag the

rotation anchor to the desired position.

3. Release the mouse to set the new rotation

anchor position.

109

Now all rotations will proceed around the

new rotation anchor position.

When moving the rotation anchor, it will

automatically lock on to atoms within the

selection as you get close to them, aiding you

in setting the rotation anchor over atom

positions.

Scaling

To scale content, perform the following steps:

1. Select the content to be scaled.

2. Hover the mouse over one of the anchor

points in the selection so that the mouse

resize cursor appears.

3. Press the mouse down and drag the

anchor to scale the content.

4. Release the mouse to finish the scale

While scaling, the x scale factor and y scale

factor will be displayed below the mouse

cursor. You can disable this feedback in the

To preserve the width-to-height ratio while

scaling content along the diagonals, just hold

down the shift key while performing the

above steps.

To precisely scale content, perform the

2. Press the Scale... menu item in the

3. Select whether to scale the content by

dimension or bond length and then

specify the rest of the settings.

4. Press the Scale button to scale the content

to the settings you provided.

Fonts

To change the fonts of atom labels and text

based shapes, perform the following steps:

1. Select the atoms and shapes that you

would like to change the fonts of.

2. Choose the font family, font size and font

style in the Files + Formatting toolbar to

change the fonts.

Drawing Aids

Drawing guides will help when precision is

important. There are several categories of

drawing guides, and each have their own

benefit. Guides can be enabled and disabled

in the Drawing Aids> submenu of the View

Atom Aids

Two types of aids can be drawn for atoms:

• Orthogonal - Will show a horizontal and

vertical line through the center of each atom

to help with alignment.

• Circular - Will show a circle around each

atom with radius equal to the current

standard bond length to help with distances.

Bond Aids

A single type of aid can be drawn for bonds:

• Parallel - Will draw a line through each

bond, parallel to its direction to help with

extrapolation.

Ring Aids

Rings can be colored in with a different color

corresponding to the size of the ring to help

with perception.

Molecule Aids

Two types of aids can be drawn for

molecules:

110

• Bounds - Will show a rectangle

representing the bounds of each molecule to

help with placement.

vertical line through the center of each

molecule to help with alignment.

Background Aids

Three types of aids can be drawn on the

background:

• Crosshair - Will render a crosshair and grid

to help with partitioning and aligning

• Grid - Will render a grid at an interval that

you specify to help with aligning objects.

• Margins - Will render the bounds for the

margins.

Colors

There are two features in the Files +

Formatting toolbar for changing the colors

of content, the Color button and the Quick

Colors button.

Color Button

The Color Button was specifically created in

ChemDoodle to make it easy to quickly

change the colors of groups of objects. There

are eight colors defined the color button:

• Background

• Borders and Lines

• Fill

• Atom Labels

• Identifier Text

• Other Text

You may change these colors by clicking the

thin rainbow button placed directly to the

right of the Color Button. All objects drawn

after choosing colors will conform to those

choices. To change the colors of a group of

objects to the current selection of colors, just

select them and click the Color Button.

The Color Button will change its display

colors to reflect the current settings. A

breakdown of the sections of the Color

Button is shown in Figure 5.2.

Figure 5.2: Color Button Layout

If you wish for a certain fill to be empty and

to not be colored, then in the color chooser,

click the Empty Color button for the desired

fills to not be painted.

Quick Colors Button

The Color Button is powerful but is certainly

not a quick way to change colors. To quickly

change colors, just use the Quick Colors

Button.

Just selected the content that you would like

colors changed for, and press the quick colors

button. All of the content will be changed to

that color regardless of the content type.

If you click and hover (or drag) over the

Quick Colors button, a palette will appear to

select a new color. Drag the mouse pointer

over one of the preset colors to select it and

111

immediately change the selected content to

that color.

You can also add custom colors to the last

three rows of the Quick Colors palette. Just

release your mouse over the circled plus icon

and release to show a color chooser.

Choose the desired color and press the OK

button to add it to the palette and change the

currently selected content to that color.

The Quick Colors palette is shown in Figure

5.3.

Figure 5.3: The Quick Colors palette.

Color Detection

When working with content that uses non

standard colors, you may wish to detect what

those colors are. To do this, expand the Quick

Colors Button and release the mouse over

the Detect Color button . Then hover

over the color in the document you wish to

detect and press the mouse down when that

color is centered in the cursor. That color will

be added to the Quick Colors Button for

further use.

Color Chooser

The color chooser will be different on all

platforms, with different templates to use to

pick colors from. However, the ChemDoodle

pinwheel color chooser will be present on all

platforms. The pinwheel color chooser is

shown in Figure 5.3.

Figure 5.3: ChemDoodleʼs Pinwheel Color

Chooser

The color selected can be seen in the preview

bar at the bottom, with the hex value shown

by default. You can also view the RGB value

by enabling the Decimal RGB checkbox.

To select a color, just move the mouse pointer

over the pinwheel until the color you would

like to select is hovered, then click the mouse.

You can also use the mouse wheel to scroll

through colors.

If the pinwheel appears all black, you will

need to increase the Brightness setting by

moving the Brightness slider up. If the

pinwheel appears all white, you will need to

decrease the Saturation setting by moving the

Saturation slider down.

112

Modifying the Z-order of

Shapes

Occasionally, you may want to change how

shapes are z-ordered with respect to each

other and with respect to atoms and bonds.

Shapes, by default, will always render behind

atoms and bonds and will be z-ordered

chronologically.

To modify the z-order of a shape, perform the

1. Hover the shape to change the z-order of.

2. Right-click on the shape.

3. Expand the Arrange submenu.

4. Select the Send Forward, Send

Backward, Send to Front or Send to

Back menu item depending on your

To change if a shape is rendered in front of or

behind atoms and bonds, perform the

4. Select the Place in Front of Structures

or Place in Back of Structures menu

item depending on your preference.

Grouping Content

Content in ChemDoodle can be grouped.

Once grouped, you will no longer be able to

edit the member objects individually. Any

transformations performed on the group will

affect all member objects.

Grouping can be nested, so groups can be

grouped into further groups. Ungrouping is

not recursive, so ungrouping a group

containing groups will leave those contained

groups intact.

Grouping

To group content, perform the following

1. Select the content to be grouped.

2. Press the Group menu item in the

Ungrouping

To ungroup content, perform the following

1. Select the groups to be ungrouped.

2. Press the Ungroup menu item in the

Removing Content

Removing individual Objects

Individual objects can be removed by using

the eraser tool to hover the object and then by

clicking to remove it. Additionally, at any

time, when an object is hovered, press the

backspace or delete key.

Removing Groups of Objects

Groups of objects can be removed in a

number of ways. You can do the following:

• Use a selection tool to select the content to

be removed. Then press the backspace or

• First select the content to be removed. Then

use the eraser tool to click on the Doodle

• Select the eraser tool, then press the mouse

down and drag over all of the content to be

removed. Selected content will be

highlighted. Then release the mouse to

remove all highlighted objects. Dragging

113

over content that has already been

highlighted will de-highlight it.

Chapter 6:

Advanced

Chemistry and

ChemDoodle is powered by an advanced

cheminformatics engine to perform several

functions for creating graphics, such as ring

perception and structure depiction. This

engine allows for some very powerful

functions to help you create your chemical

graphics and to analyze the structures you

draw.

advanced structure functionality within

ChemDoodle. It introduces the following

• The cheminformatics algorithms

implemented in ChemDoodle.

• How to use these functions to perform

various advanced tasks.

• How to edit your structures in a more

advanced way than described in Chapter 3.

• How to take full advantage of the functions

provided in ChemDoodle.

Aromaticity

Aromaticity is detected based on the Hückel

model. All rings are assumed to be planar.

Any appropriately hybridized heteroatoms

can be constituents in an aromatic ring.

114

Representations for Aromatics

To toggle between viewing aromatics in

Kekulé form (with double bond lines) or with

circles, perform the following steps.

1. Open the Preferences window.

2. Select the Rings tab under the Visuals

3. Check or uncheck the Use Circles visual

specification under the Aromatics section

based on your preference.

Forcing Aromaticity

In rare cases, ChemDoodle may determine a

ring to have no aromatic character when it

should be aromatic for some purpose. To

force a ring to be recognized as aromatic,

change all of the ring bonds to Resonance

Calculating Covalent Bonds

Some chemical input read into ChemDoodle

may not include bond topology such as PDB

and XYZ files as well as some output from

modeling programs. Instead of having to

define the bonds by hand, ChemDoodle

contains tools for deducing covalent bonds

based on published covalent radii.

To deduce covalent bonds, perform the

1. Select the atoms that you would like

covalent bonds deduced between.

2. Select the Calculate Covalent Bonds

menu item from the Structure menu.

Covalent radii are a best fit from a large

number of experimental covalent radii. In

some cases, a bond distance from a file may

be larger than the distance calculated by

adding the corresponding element covalent

adii together and the bond will not be found.

To address this, ChemDoodle multiplies all

covalent radii by a scalar when deducing

bonds. By increasing this multiplier,

ChemDoodle will discover bonds at longer

distances. You can change the radius

multiplier in the Preferences window under

the Functions tab.

Carbon Labels

By default, ChemDoodle draws skeleton

figures where carbon labels are suppressed.

Regardless, it may be necessary to show the

carbon label for various reasons and this can

be done easily for each atom or globally for

all atoms. To affect this globally, change the

following visual specification for the

document style sheet in the Preferences

window. For each atom, change the following

visual specification in the atom’s Format

The atom Display Carbon Label visual

specification has 4 options for displaying

carbon labels:

• Always - always display the “C” for the

carbon label.

• On Lone and Hidden - only display carbon

labels on lone and hidden carbons.

• On Hidden - only display carbon labels on

hidden carbons. (default)

• Never - never display “C” labels.

The default is On Hidden and only carbon

atoms that are “hidden” between two bonds of

the same bond order will have their label

displayed as shown in Figure 6.1.

Figure 6.1: Hidden carbon labels are shown.

115

Lone carbons are disconnected atoms and

have no bonds attached.

In addition to manually changing this visual

specification, there is a quick method

provided to show/hide carbon labels. To

quickly show individual carbon labels,

1. Hover the carbon atom with label to be

shown.

2. Right-click on the atom and select the

Show Carbon Label menu item.

To hide the carbon label. Perform the same

steps, but instead select the Hide Carbon

Label menu item.

Terminal Carbon Labels

By default, all terminal carbon atoms will

display labels. In some cases, these labels

may clutter a diagram. To hide terminal

carbon labels, uncheck the Show Terminal

Labels visual specification in the Carbons

section in the Atoms section in the Visuals

section of the Preferences window.

Chemical Suppliers

Chemical suppliers for the structures you

draw can be listed by performing the

1. Draw the structure you would like to

search for.

2. Select the structure with a selection tool.

3. In the Structure menu, expand the

Chemical Suppliers menu item.

4. Select the Substructure Match or Exact

Match menu item depending on whether

you want to search for a substructure or

exact match for the selected structure.

5. The ChemExper database will appear in

your default browser with a listing of

matches. Select the match to view the

chemical suppliers.

The ChemExper database provides the

supplier information and you must abide by

their terms of use and any copyrights or

disclaimers presented when using their

service.

Chemical Warnings

ChemDoodle will check your structures for

you and flag any questionable objects.

Warning Types

The following warnings are currently

implemented:

• Improper Valency - It is unlikely that this

element can have the current coordination

number. Or the atom label is an

abbreviation and the valency is

overextended.

• Uninterpretable Label - ChemDoodle

does not understand or interpret the text

present in the atom label as chemically

relevant.

• Unpublished Mass Number - This mass

number is not found in ChemDoodle’s

database of published isotopes for the

element.

• Unpublished Oxidation State - The

oxidation state of this atom is not found in

ChemDoodle’s database of published

oxidation states for the element.

• Sum of Bonds is not an Integer - The

coordination number of this atom is not a

whole number.

116

• Questionable Stereochemistry - The

stereochemistry of this atom is

questionable.

• Atom Overlaps Another - This pair of

atoms has the same coordinates and will be

perceived as a single atom in graphical

output.

Disabling Warnings Globally

These warnings can be disabled individually

Warnings tab as shown in Figure 6.2. This

tab also contains an option to disable the

display of chemical warning explanations at

the top-left of the document the warnings are

present in.

Figure 6.2: Chemical Warnings

To disable warnings on a single atom,

1. Hover the atom with the warning shown

to be disabled.

Ignore Warnings menu item.

To reenable warnings for an atom that is

ignoring warnings, just right-click on it after

hovering it and select the Check for

Warnings menu item.

Hiding Warnings from Rendering

Chemical warnings will never appear in any

image output or printouts.

If the warnings clutter the document while

drawing, they can be easily suppressed by

selecting the Hide Warnings menu item in

the View menu.

Cleaning Structures

ChemDoodle can generate 2D and 3D

coordinates for structures.

Optimizing Structures in 2D

If your structures do not have acceptable or

aesthetic coordinates, ChemDoodle can clean

them. To clean your structures, perform the

1. Select the structures to be cleaned.

2. Expand the Clean submenu in the

Structure menu and select the 2D

Optimization menu item.

ChemDoodle employs the published CCG

algorithm for cleaning structures. This

method is a statistical approach. Therefore,

repeated applications of the function may

produce different results. If you are not happy

with the first result of the function, try it

again, something better may be generated.

Distance Geometry Embedding

Distance geometry embedding sets 3D

coordinates for a structure based on a

regression of its bond distance matrix. This

function works best on highly embedded

structures such as fullerenes and carbon

nanotubes. To use this method, perform the

117

1. Select the structures to generate 3D

coordinates for by distance geometry

embedding.

Structure menu and select the Distance

Geometry Embedding menu item.

Preserving Stereochemistry

By default, structure cleaning will preserve

stereochemical configurations. To disable

this, deselect Clean Retains

Stereochemistry in the Functions panel in

Preferences.

Descriptors

ChemDoodle calculates a large number of

molecular descriptors. The descriptors are

currently categorized into 4 types:

constitutional, topological, physicochemical

and ADME.

Constitutional

Constitutional descriptors are based on the

makeup of the molecule, such as atom counts

and molecular formula. The following

constitutional descriptors are provided:

• Atom Count - The number of atoms in a

• Bond Count - The number of bonds in a

• Degree of Unsaturation - The sum of all

bond orders substracting 1 for each, plus the

number of rings.

• Element Counts - The number of each

element that is present in a molecule.

• Euler Facet Ring Count - The count of all

Euler facets in a molecule. This is defined

as all of the sides of the 3D shape that is

created by expanding the 2D structure on a

• Exhaustive Ring Count - The total number

of graph cycles present in the molecule.

• Frèrejacque Number - The fundamental

ring count. Also known as the cyclomatic

number or the SSSR count.

• Hydrogen Bond Acceptor Count - Counts

the number of atoms with lone pairs capable

of hydrogen bonding.

• Hydrogen Bond Donor Count - Counts all

Nitrogens, Oxygens and Fluorines that have

Hydrogens attached.

• Rotatable Bond Count - Counts all

saturated bonds. Exceptions are Single

bonds connected to Hydrogens or terminal

atoms, Single bonds of amides, thioamides,

sulphonamides and those connecting two

hindered aromatic rings (having at least

three ortho substituents).

• Total Electron Count - Counts all

electrons in a molecule. Takes into account

charges.

• Lightest Isotopic Mass - Calculates the

lightest isotopic mass by summing the

lightest isotope for each atom given its

• McGowan Characteristic Volume -

Calculates the vdW volume with

McGowan’s method.

• Molecular Mass - Calculates the molecular

mass from atomic masses based on the

IUPAC technical reports.

• Monoisotopic Mass - Calculates the

monoisotopic mass from isotopic masses

based on the IUPAC technical reports.

118

• Volume as a Sum of Atomic and Bond

Contributions - Calculates the VABC

vdW volume.

empirical formula for the molecule. The

empirical formula is just the molecular

formula, where all element multiplicities

have been divided by the greatest common

denominator.

molecular formula for the molecule in the

form of CxHy... where ... denotes all other

elements and their counts in alphabetical

order. This is based on the Hill system, so if

no carbon atoms are present, the hydrogen

count will be in alphabetical order with the

rest of the elements.

Topological

Constitutional descriptors are solely based on

the connectivity between atoms in a molecule,

such as a bond distance matrix. The following

topological descriptors are provided:

• Centric Index - Calculates the Centric

index for the molecule (Bonchev et al.).

topological distance in a molecule.

• Hosoya Index - Calculates the Hosoya

index for the molecule.

• Molecular Topological Index - Calculates

the Molecular Topological index for the

molecule (Schultz et al.).

• Platt Index - Calculates the Platt index for

• Ring Complexity - Calculates the Ring

Complexity for the molecule.

• Szeged Index - Calculates the Szeged index

for the molecule.

• Wiener Index - Calculates the Wiener

• Zagreb Indices - First and second order

calculations are supported. (Z1, Z2)

• Balaban Index - Calculates the Balaban

• Bertz Complexity Index - Calculates the

Bertz Complexity index for the molecule.

Branching index for the molecule. The

Branching index is equivalent to 1 χ.

• Chi Molecular Connectivity Indices -

Indices from zeroth to third order are

supported. Both simple and valence models

are calculated. ( 0 χ, 1 χ, 2 χ, 3 χ, 0 χv, 1 χv, 2 χv, 3 χv)

Framework (fMF) ratio for the molecule.

• Harary Index - Calculates the Harary

• Kappa Shape Indices - Indices from the

first to third order are supported. Both

simple and alpha models are calculated. ( 1 κ,

2 κ, 3 κ, 1 κα, 2 κα, 3 κα)

• Superpendentic Index - Calculates the

Superpendentic index for the molecule.

• Adjacency Matrix - Generates a matrix M

of size AxA, where A is the number of

atoms in the molecule. M(Ai, Aj) equals 1 if

there is a bond connecting atoms i and j,

and equals 0 otherwise.

• Bond Distance Matrix - Generates a

matrix M of size AxA, where A is the

number of atoms in the molecule. M(Ai, Aj)

equals the the number of electrons shared

between atoms i and j.

119

• Bond Electron Matrix - Generates a

equals the shortest bond distance between

atoms i and j.

• Detour Matrix - Generates a matrix M of

size BxA, where B is the number of bonds

in the molecule and A is the number of

atoms in the molecule. M(Bi, Aj) equals 1 if

bond i contains atom j, and 0 otherwise.

• Incidence Matrix - Generates a matrix M

atoms in the molecule. M(Ai, Aj) equals the

longest bond distance between atoms i and

j.

• Laplacian Matrix - Generates a matrix M

and equals 0 otherwise. M(i,i) equals the

number of bonds connected to atom Ai.

Physicochemical

Constitutional descriptors describe the

physical or chemical properties of a molecule.

These are estimations of their real physical

values. The following physicochemical

descriptors are provided:

• Average Molecular Polarizability -

Estimates the average molecular

polarizability. Both the average hybrid

components (Miller) and average hybrid

polarizabilities (Kang) methods are

implemented.

• Critical Pressure - Estimates the critical

pressure (Pc) of a substance based on

Joback’s method.

• Critical Temperature - Estimates the

critical temperature (Tc) of a substance

based on Joback’s method.

• Critical Volume - Estimates the critical

volume (Vc) of a substance based on

• Enthalpy of Formation - Estimates the

enthalpy of formation (ΔH 0 f,298) of a

substance (ideal gas at 298K) based on

• Enthalpy of Fusion - Estimates the

enthalpy of fusion (ΔHf) of a substance

based on Joback’s method.

• Enthalpy of Vaporization - Estimates the

enthalpy of vaporization (ΔHvb) of a

substance (at Tb) based on Joback’s method.

• Gibbs Energy of Formation - Estimates

Gibbs energy of formation (ΔG 0 f,298) of a

substance (ideal gas, unit fugacity, at 298K)

• Heat Capacity - Estimates the heat

capacity(C 0 p) of a substance (ideal gas)

• Lipophilicity, logP - Estimates the octanol/

water partition coefficient (logP) of a

substance. The NC+NHET, AlogP98, and

XlogP v2.0 (Wang) algorithms are

• Liquid Viscosity - Estimates the liquid

viscosity (ηL) of a substance (at 298K)

• Molar Refractivity - Estimates the molar

refractivity of a substance. Both the CMR3

and AMR algorithm are implemented.

• Normal Boiling Point - Estimates the

normal boiling point (Tb) of a substance

• Normal Freezing Point - Estimates the

normal freezing point (Tf) of a substance

120

Estimates the topological polar surface area

(TPSA) of a molecule with the algorithm

developed by Ertl et al.

ADME

Descriptors that rank bioactivity of drugs

(ADME stands for absorption, distribution,

metabolism, and excretion):

• Bioavailability Score - Calculates the

bioavailability score (Martin).

• Egan Violations Count - Calculates the

number of violations to Egan’s rules.

• Lipinski’s Rule of 5 Violations Count -

Counts the number of violations to

Lipinski’s rule of 5.

• Veber Violations Count - Calculates the

number of violations to Veber’s rules.

Flattening Atomic Coordinates

In cases where imported chemical data

contains 3D coordinates, you can set all the zcoordinates

to 0 by selecting that content and

choosing the Flatten menu item in the

Fragmentation

ChemDoodle contains several functions for

fragmenting molecules with various results.

The fragmentation functions can be found in

the Content toolbar .

There are three fragmentation functions:

• Molecular Weight - The molecules

will be fragmented and each fragment will

have a molecular weight assigned.

• Synthesis - The molecules will be

fragmented and each fragment will be set as

a reactant in a synthetic reaction leading to

the original molecules.

• Retrosynthesis - The molecules will

be fragmented and each fragment will be set

as a product in the retrosynthetic reaction

resulting in the original molecules.

To fragment a molecule or group of

molecules, perform the following steps:

1. Select the desired fragmentation function

in the Content toolbar.

2. Press the mouse down and drag over all

the bonds to be removed, defining how

the molecule is fragmented.

3. Release the mouse to complete the

function.

Formal Charges

While you can place charges on atoms

manually, ChemDoodle can also guess the

formal charges for a structure. To have

ChemDoodle guess formal charges for a

structure, perform the following steps:

1. Select the atoms for which formal charges

are to be guessed.

2. Choose the Place Formal Charges menu

Glassware Clipart

Figures for glassware setups can be created

by using the glassware clipart library within

To build glassware setups, perform the

1. Click on the Laboratory Glassware

121

2. In the window that appears, select a

glassware piece that you would like to

place into your figure.

3. Press the mouse down on the current

document and drag to place it where you

prefer the piece to be placed. Hold down

the shift key to flip the template

horizontally while placing.

4. Release the mouse to set the glassware

piece.

5. Repeat steps 2-4 until your figure is

complete.

It may prove necessary to be conscious of the

order in which you place the glassware pieces

in the figure, in order to show some piece

over another.

Keep in mind that each template is a complete

image, and it is not possible to show one

piece in between the front and back of

another piece. However, you may export your

figure to be post-edited in vector editing

software (such as Adobe Illustrator) to

achieve this effect.

All glassware clipart is governed by the same

visual specifications that other shapes are. So

you can change the stroke thickness and the

colors of the various components in the

clipart as shown in Figure 6.3.

Figure 6.3: A glassware setup with altered colors.

Flipping Glassware

To flip the clipart graphics, just hold down the

shift key while placing them. The preview

will then show you the flipped graphic.

You can also manually edit whether a clipart

is flipped or not by right-clicking on it with

nothing selected, selecting the Format

Clipart... menu item and then changing the

Flip on/off choice in the Clipart section.

Tubing

You may wish to connect pieces of glassware

via tubing. A good technique for doing this is

by using the Bezier Curve tool to draw the

path of the tubing, and then increasing the

stroke width of the path to the desired

thickness.

One method for doing so is as follows:

122

1. Select the Bezier Curve tool in the

2. Press the mouse down in the middle of the

outlet in the glassware figure where the

first tubing connection will be made.

3. Drag the mouse out in the direction that

the first outlet faces. The longer you drag

out the control point, the longer the curve

will be straight at that point.

4. Press the mouse down in the middle of the

second tubing connection will be made.

5. Drag the mouse out in the direction that

the second outlet faces. The longer you

drag out the control point, the longer the

curve will be straight at that point.

6. Edit the bezier curve if necessary, or press

the escape key to finish drawing the

curve.

7. Hover the curve using a selection tool and

right-click, selecting the Format Bezier

Curve... menu item.

8. In the Strokes section of the settings

window that appears, change the

Thickness setting to 10 pixels.

9. Select the Done button to close the

settings window.

Your completed figure will then contain a

nice smooth curve connecting the outlets that

represents tubing as shown in Figure 6.4.

Figure 6.4: Glassware figure containing tubing

Graph Reduction

To reduce molecule graphs, perform the

1. Select the structure with the graphs you

would like to be reduced.

2. Expand the Graph Reduction submenu

in the Structure menu and select the

preferred reduction method.

Reduce 0° (Lone)

Will remove all selected atoms that have no

bonds attached.

Reduce 1° (Terminals)

Will remove all selected atoms that have only

1 bond attached to them. This process will

stop after the first iteration.

Repeatedly Reduce 1°

continue until it has pruned all terminal

chains from the selection.

123

Reduce 1° + 0°

Will remove all selected lone and terminal

Reduce 2° (Chains)

Will remove all chains from a molecule,

leaving single bonds connecting any

remaining 3° atoms.

Reduce 2° + 1° + 0°

Will remove all lone, terminal and chain

atoms, leaving a simplified core that

represents the embedded ring structure of a

graph.

Hydrogens

Hydrogens do not need to be drawn on

structures as they are implicitly declared. At

any time, Hydrogens can be added to a

structure as text in atom labels or as atoms

with bonds attached.

Implicit Hydrogen Rendering

By default, implicit hydrogens are

automatically rendered on any element labels

that are visible.

To disable the auto-rendering of implicit

hydrogens, uncheck the Show Implicit

Hydrogens visual specification in the

Hydrogens section of the Atom section of

the Visuals tab in the Preferences window.

You can also disable the auto-rendering of

implicit hydrogens for a specific atom by

1. Hover the atom with implicit hydrogens

to remove.

2. Right-click on the atom.

3. Select the Hide Implicit Hydrogens

This will stop the auto-rendering of implicit

hydrogens on that atom. To restore the

implicit hydrogen auto-rendering, just follow

the same steps as above, but choose the Show

Implicit Hydrogens menu item.

Adding Hydrogens as Atoms

To add hydrogens to a structure as atoms as

shown in Figure 6.5, perform the following

1. Select the structure to add hydrogens to.

2. Expand the Add/Remove Hydrogens

submenu in the Structure menu and

select the From Selection menu item.

Figure 6.5: Hydrogens added as atoms

Adding Hydrogens as Text

To add Hydrogens as text into atom labels as

shown in Figure 6.6, change the Add as

setting in the Hydrogens section in the

Preferences window, under the Visuals tab,

under the Atoms tab to Text. Now when using

the Add/Remove Hydrogens functions,

hydrogens will be explicitly added as text.

Figure 6.6: Hydrogens added as text

to Carbons

You can modify how hydrogens are added to

carbon atoms: whether they are always added,

only added to unsaturated carbons or never

added to carbons. These options are presented

in the Preferences window, under the Visuals

tab, under the Atoms tab in the Carbons

124

IUPAC Naming

Currently only generating a structure from an

IUPAC name is supported.

Name to Structure

To parse an IUPAC name and generate a

chemical structure, perform the following

1. Select the Parse IUPAC Name... menu

item from the Structure menu.

2. In the prompt that appears, input the

IUPAC name and select the Accept

The generated structure will then be placed in

Kekulé Structures

ChemDoodle contains a function for

assigning Double bonds to a structure such

that pi electron delocalization is maximized.

Both frames of Single bonds and

substructures consisting of only Resonance

bonds can be affected.

Kekulizing a Single Bond Frame

To easily draw Kekulé structures, you may

begin by just drawing a Single bond frame.

This way, ChemDoodle can optimally assign

Double bonds to the structure. If there are

other bond types present, ChemDoodle will

not Kekulize the structure. However, the

Saturate function in the Structure menu will

change all bond types to Single bonds.

To Kekulize a structure of only Single bonds,

1. Select the structure containing only Single

bonds to be Kekulized.

2. In the Structure menu, select the

Kekulize menu item.

For example, corannulene is generated from a

Kekulization of a Single bond frame in Figure

6.7.

Figure 6.7: Kekulizing a Single bond frame to

generate corannulene.

Resonance Bonds

In some cases, structures may be read in with

Resonance bonds. It may be necessary to

present a Kekulé structure instead of the

resonance model. When Kekulizing a

structure with Resonance bonds, only those

Resonance bonds will be affected.

To Kekulize a substructure of Resonance

bonds, perform the following steps:

1. Select the structure containing the

substructure of Resonance bonds to be

Kekulized.

Kekulize menu item.

For example, the aromatic rings in Viagra are

Kekulized in Figure 6.8.

Figure 6.8: Kekulizing the aromatic rings in the

resonance model for Viagra.

Label Expansion

Atom labels can be much more than just an

element symbol. They may contain implicit

125

hydrogens or chemical shorthand notations or

abbreviations. ChemDoodle can expand these

condensed labels to their all atom models.

Expanding Labels

To expand labels, perform the following

1. Select the atoms with labels to be expanded

using any of the selection tools.

2. Select the Expand Labels menu item in

the Structure menu.

Implicit Hydrogens

Implicit hydrogens can be presented as text in

an atom label. They may be added

automatically, can be added manually using

the Atom Label tool or globally using the

Add/Remove Hydrogens function with the

appropriate visual specifications set.

When expanded, implicit hydrogens are

ignored. So the label NH2 will become a N

label when expanded.

Condensed Labels

Chains and functional groups may be denoted

with a condensed label. For instance, a

carboxy group may be denoted by a COOH

atom label or an ethyl group may be denoted

by CH2CH3.

When expanded, condensed labels will be

replaced by the all atom model of the

fragment as shown in Figure 6.9.

Figure 6.9: Left a molecule with condensed atom

labels; right the corresponding expanded

Several constructs are supported by the

condensed interpreter in ChemDoodle:

1. Linear Chains - Stringing elements

together will place them in a chain, so

CCCC or CH2CH2CH2CH3 denotes a nbutyl

group.

2. Multiple Attachments - Using parenthesis

will denote multiple attachments, so the

label C(CH3)3 will denote a t-butyl group.

3. Single and Double Bonds - If no bonds

are placed between elements, then Single

bonds are used to connect them. The -

(minus) character will also specify a Single

bond connection and the = (equals)

character will specify a Double bond

connection. Therefore, CC and C-C both

specify an ethyl group while C=C will

specify an vinyl group.

Abbreviations

In addition to condensed formulas,

abbreviations can be used to define fragments

in atom labels. For instance, the Ph

abbreviation defines a phenyl group. All

supported abbreviations are listed in the

Symbols widget in the Abbreviations section.

When expanded, abbreviations will be

replaced by the all atom model they define as

shown in Figure 6.10.

Figure 6.10: Left a molecule with abbreviations;

right the corresponding expanded structure.

ChemDoodle can only expand abbreviations

that represent discrete molecules, monovalent

or divalent fragments. ChemDoodle will

attempt to interpret abbreviations properly

based on their valency. For instance, the CO2

abbreviation with a valency of 0 is a carbon

126

dioxide molecule while that same label with a

valency of 2 denotes a ester group.

Adding Custom Abbreviations

Custom abbreviations can be added by

1. Select the Add New... menu item in the

Abbreviations submenu of the Structure

2. Type the abbreviation label to be used in

atom labels in the Abbreviation Label text

field.

3. Type the full name of the abbreviation in

the Full Description/Name text field.

4. Provide the SMILES string for the full

atom model of the abbreviation in the

SMILES for Abbreviation text field. If the

valency of the abbreviation is greater than

0, then the attachment atom is the first

atom defined by the SMILES string. If

the abbreviation is divalent, then the last

atom defined in the SMILES string will

be used as the second attachment atom.

5. Select the valency of the abbreviation

using the Valency drop down selection.

6. Press the Add button to add the new

abbreviation.

ChemDoodle will update to recognize the

added abbreviation and when used, that

abbreviation will be expanded to the

SMILES string defined.

Abbreviations and condensed notations can

be combined. So the atom label CPh3 will

denote a triphenylmethyl group.

Molecular Formulas

Sometimes you may intend to input a

molecular formula into an atom label, to

calculate a molecular weight, for instance. If a

molecular formula is input, then ChemDoodle

will associate that atom with an isomer of the

molecular formula, as best as it can as shown

in Figure 6.11. So your calculations of weight

will be correct, but other calculations will

have to be met with scrutiny. For accurate

calculations, make sure to draw a correct

structure or structural formula.

Figure 6.11: ChemDoodle expands a molecular

formula to an isomer all atom model as best as it

can.

Newman Projections

To build graphics for Newman Projections,

1. Draw a 2-methylpropane structure.

2. Hover the central atom and right-click.

3. Select the Show Carbon Label menu

4. Again, hover the central atom and rightclick.

5. Select the Format Atom... menu item.

6. In the Elements section, select the Use

Circles checkbox, make sure Coloring is

set to User Chosen and Radius

Convention is set to Constant, and then

set the Constant Radius to the preferred

size. You will now see a black circle

appear over the central carbon.

7. Still in the Atom Settings window, under

the Colors section, change the Text Color

to white. You should now see a figure just

like Figure 6.12.

127

Figure 6.12: A half completed Newman Projection.

8. Click on the Done button exit the Atom

Settings window.

9. Draw a second 2-methylpropane structure.

10. Rotate the second structure to the desired

torsion for the Newman Projection.

11. Using a lasso tool, move the second

drawn structure over the first to complete

the Newman Projection.

Figure 6.13: A finished Newman Projection.

You can then edit the terminal labels to

display the structure desired as is shown in

Figure 6.13. It may be convenient to save a

copy of this structure as a file for later use.

Ring Perception

Rings are cycles of atoms and are important,

because ChemDoodle uses them to define

graphics such as which direction double

bonds face and calculations such as

aromaticity detection. There are several

published algorithms to define rings in

structures producing different ring sets.

Supported Ring Sets

Currently, ChemDoodle can perceive the

following sets:

• Smallest Set of Smallest Rings - The

smallest set of smallest rings (SSSR) is the

standard for defining ring sets in flat 2D

structures.

• Euler Facet Rings - The Euler facet ring

set is better than the SSSR at defining

structures. It is defined by all the rings that

make up the faces of a 3D object when the

2D chemical graph is placed on a 3D

sphere.

• Hanser (All) Rings - Every last graph cycle

in selected structures.

Exploding Ring Sets

Ring sets can be exploded from the structure.

In other words, they will be laid out around

the structure to show the rings and where they

are contained. To explode ring sets, perform

1. Select the structures with the rings to be

exploded.

2. Expand the Rings submenu in the

Structure menu and select the Explode

Smallest Set of Smallest Rings, Explode

Euler Facet Rings or Explode Hanser

(All) Rings menu items.

In very complex structures, the exploded ring

diagram will be highly overlapped. Just stack

the rings (in the Content menu) to view them

all clearly.

Performance Considerations

If dealing with heavily embedded structures,

such as zeolites or MOFs, the algorithms may

become very cpu intensive. In these cases,

you can disable deep searching for rings by

selecting Ring Search Cutoff in the

Functions panel in Preferences.

Sequence Tool

ChemDoodle provides a tool for generating

sequence structures for common polymer

types. The following polymer types are

supported:

128

1. Three Letter Amino Acid Sequence

To generate sequences, use the Sequence tool

in the Shapes toolbar. To draw a

sequence, perform the following steps:

1. Click on the current document where you

want the sequence to originate from. The

endpoints of the sequence will appear. For

amino acid sequences, a water molecule

will appear.

2. A single atom will be surrounded by a

blue circle; this is the appending atom. All

changes to the sequence append directly

to this atom. You can hover over other

atoms and click to set a new appending

3. Use the keyboard to type the one letter

hotkeys for the residues in the sequence

set. For instance, pressing the A key will

append an Alanine residue, and pressing

the R key will append an Arginine residue.

Sequences will automatically wrap to stay

within the margins of the current document as

shown in Figure 6.14.

Figure 6.14: A wrapped sequence for Crambin.

Use this tool to easily create macromolecular

structures, and to quickly calculate properties

such as weights and isotopic distributions.

Stereochemistry

The stereochemistry of chiral centers and

double bonds can be determined by selecting

the Stereochemistry functions located in the

Structure menu. An Attribute object will be

associated with the stereocenter to denote the

stereochemical configuration. Several

conventions can be used. Centers can be

forced into a particular configuration in

addition to determining the configurations

based on the 2D layout.

Chiral Centers

Cahn-Ingold-Prelog (CIP) priority rules are

used to resolve rectus (R) and sinister (S)

enantiomers.

Forcing a configuration will interchange the

protruding and recessed bonds, if necessary.

If only single bonds are present, then the

appropriate wedge bonds will be placed when

a configuration is forced.

Double Bonds

CIP priority rules are used to resolve

entgegen (E) or zusammen (Z) configurations

around double bonds. The less systematic cis/

trans conventions can also be used to define

olefin enantiomers. The E/Z system will work

for any double bond presented, while the cis/

trans conventions will not return results in

ambiguous cases.

Forcing Double bond stereochemistry will

flip both substituents on one atom's side of

the double bond through the double bond

axis, if necessary.

Resolving Stereochemistry

To resolve stereochemistry for structures,

1. Select the structures or parts of structures

with stereocenters to be resolved with the

2. Expand the Stereochemistry> submenu

in the Structure menu.

3. Choose the appropriate Assign menu item

to resolve stereocenters of that type.

129

You may also access these functions through

the right-click menu.

Configurations

To force a stereochemical configuration on an

atom or bond, perform the following steps:

1. Hover the atom or bond on which the

configuration will be forced.

2. Right-click on the hovered object.

3. If that object is a potential stereocenter,

then the Stereochemistry> submenu will

be present. Expand this submenu.

4. Choose the appropriate Force menu item

to force the configuration.

Structure Perspective

Even though ChemDoodle generates graphics

for structures in two dimensions, the

underlying structures are defined in three

dimensions.

ChemDoodle will read in 3D coordinates

from all chemical files and provides functions

for rotating structures in 3D.

NOTE: While ChemDoodle has some 3D

editing features, it is not a molecular

modeler and is not the appropriate choice

to build 3D coordinates for structures.

To rotate structures in 3D, perform the

1. Select the structures to be rotated in 3D

using the selection tools.

3. Click the mouse down and drag to rotate

the structure in 3D.

4. Release the mouse to finish the action.

By default, mouse movements while rotating

structures in 3D will rotate the structure

around the x and y axes based on horizontal

and vertical movement respectively. You can

also set the 3D rotations to be defined by a

quaternion trackball in the Preferences

Just like when rotating structures in 2D, there

will also be a rotation anchor present during

3D rotation. Before selecting the 3D rotation

tool, you can move the rotation anchor to a

helpful position than the center, such as over

atom positions. This makes it easy to rotate

structures around atoms in 3D space.

Unique IDs

IDs can be automatically added as attributes

for atoms and bonds. To do so, just select the

appropriate choice in the Unique IDs>

submenu in the View menu.

Zero Order/Ionic Bonds

In some cases, a molecule may contain ionic

bonds or you may wish to associate two

atoms that are not connected with a covalent

bond.

ChemDoodle contains a zero/ionic bond order

specifically for these cases. You can use this

bond order by selecting the Zero/Ionic bond

type button in the Bonds toolbar. Any

atoms connected with this bond type will be

spatially linked and can be sent to

cheminformatics algorithms such as

molecular formula generation and structure

cleaning.

Note: Most filetypes have no concept of a

zero order bond, so saving these bond

types and loading them into other

applications may not produce desired

results.

Chapter 7:

Reactions

Reactions can be drawn in ChemDoodle

using structures and arrow shapes. Almost

any type of reaction or mechanism can be

drawn. ChemDoodle also contains tools for

explicitly defining reactions for various

purposes.

reactions within ChemDoodle. It covers the

• How to draw reactions.

• How to draw mechanisms.

• What types of arrows can be drawn.

• How to build and define reactions and

reaction schemes.

• How to edit reactions.

• How to clean reactions.

Drawing Reaction Arrows

Reaction arrows are created from basic arrow

shapes. Instructions for drawing arrow shapes

are provided in Chapter 4.

Arrow Types

Many different types of arrows can be easily

created using the Arrows toolbar described in

Chapter 2. This section briefly goes over the

different styles and presets.

Arrowhead Styles

Arrowhead styles can be set to both the start

and end of the arrow. Several arrowhead

131

styles (half-heads) can be flipped over the

arrow axis. The following arrowhead styles

are provided:

• Full Indented -

• Full -

• Unfilled Full Indented -

• Unfilled Full -

• Chevron -

• Half Indented -

• Half -

• Unfilled Half Indented -

• Unfilled Half -

• Hook -

Both the arrowhead length and angle can be

changed to match any look. To change the

arrowhead length and angle, perform the

1. Hover the arrow containing the arrowhead

to be edited.

2. Right-click on the arrow and select the

Format Line... menu item.

3. Scroll down to the Reaction section in the

Format Line window that appears.

4. In the Arrow at Start and Arrow at End

sections, use the Length and Angle

sliders to edit the arrowheads.

Quickly Toggle Arrowheads

Instead of opening the shape settings window,

you can easily toggle default arrowheads on

the ends of objects that support arrowheads

by hovering the object and pressing the left

arrow (to toggle start) or right arrow (to

toggle end) keys.

Connector Styles

A connector is the line that connects the start

and end arrows, if any. The following

connector styles are provided:

• Solid -

• Dashed -

• Wavy -

• Doubled -

• No Go (cross) -

• No Go (slash) -

• Rearrangement -

Special Arrow Presets

Many different types of arrows can be drawn

with Arrows toolbar. The following describes

how these tools build common arrow types.

Reaction Arrow - A reaction arrow

is the default style and is drawn with no start

arrow, a Full Indented end arrow and a Solid

connector.

Retrosynthetic Arrow - A

retrosynthetic arrow can be drawn with no

start arrow, a Chevron end arrow and a

Doubled connector. The default arrowhead

angle and length is not aesthetic for this type

of arrow, so use the retrosynthetic preset in

the presets group button to quickly access this

Equilibrium Arrow - An

equilibrium arrow can be drawn with a Half

Indented start arrow, a Half Indented end

arrow and a Doubled connector. The double

line spacing can be edited in the arrow’s

visual specifications.

132

Resonance Arrow - A resonance

arrow can be drawn with a Full Indented

start arrow, a Full Indented end arrow and a

Solid connector.

Electron Pair Shift - A shift of an

electron pair can be drawn with no start

connector. Then select the appropriate arc

angle for the figure.

Single Electron Shift - A shift of a

single electron can be drawn with no start

arrow, a Half Indented end arrow and a Solid

Photon - A photon can be drawn

with a Full end arrow and a Wavy connector.

Bold - A bold arrow can be drawn

with no start arrow, an Unfilled Full end

arrow and a Doubled connector. The default

arrowhead angle and length is not aesthetic

for this type of arrow, so use the

retrosynthetic preset in the presets group

button to quickly access this type.

Bezier Arrow Ideas

In addition to straight and arced arrows, some

pretty complex arrow shapes may be drawn

with the bezier tools. The following are a few

ideas. Just mimic the location of the control

points to match them.

The Chute Arrow

The Loop Arrow

The Escalator Arrow

The Hump Arrow

The Zigzag Arrow

Building Reactions

Reaction figures can be drawn by placing

structures next to arrow shapes to describe

reaction schemes. This method will create a

visual diagram for the reaction, but

133

underlying semantics will not exists. In other

words, there is no formal definition of the

reaction reactants or products.

To address this, ChemDoodle provides a

reaction building system to explicitly define

reactions and reaction schemes.

Implicitly

To implicitly define a reaction, perform the

1. Draw the arrow you would like to

represent the reaction arrow.

2. Draw any reactants and place them to the

left of the arrow shape.

3. Draw and products and place them to the

right of the arrow shape.

4. Select the arrow shape and all reactants

and products using the selection tools.

5. Press the Build Implied Reaction menu

item in the Reaction menu to define the

reaction.

All structures with midpoints to the left of the

arrow shape’s midpoint will be defined as

reactants in the reaction while all structures

with midpoints to the right of the arrow

shape’s midpoint will be defined as products

in the reaction.

Explicitly

To explicitly define a reaction, first select the

arrow shape you would like to represent the

reaction arrow using the selection tools. Then

press the Edit Reaction… menu item in the

Reaction menu open the Edit Reaction

window for that selected arrow, as shown in

Figure 7.3.

The Edit Reaction window is a drag and

drop interface. All molecules in the current

document are displayed in the bottom tray,

while the left and right trays correspond to the

constituent reactants and products

respectively. Just drag and drop molecules

from the bottom tray into the other two to set

up the reaction. Once a molecule has been

placed, it will be grayed out in the bottom

tray and no longer selectable. You can transfer

a placed molecule between the products and

reactants by dragging the molecule between

the side trays. You can remove a molecule

from the reaction completely by dragging and

dropping it back in the bottom tray.

Press the Done button in the Reaction

Builder window to set the reaction.

Adding Reaction Conditions

To add reaction conditions above and below

the reaction arrow, first select the arrow shape

you would like to add conditions to using the

selection tools. Then press the Edit

Reaction… menu item in the Reaction menu

open the Edit Reaction window for that

selected arrow, as shown in Figure 7.3.

The Edit Reaction window contains two text

editors for adding text above and below the

reaction arrow. Click on a text area and type

to add text. You can format the text using the

text formatting tools above the text areas.

Use the Symbols widget to input characters

into the reaction condition text areas that are

not present on the keyboard.

Adding Plus Symbols

After building a reaction, plus symbols will

automatically be added at the midpoints

between the constituent reactants and

products. This feature can be turned off in the

under the Reactions tab as shown in Figure

7.2. Just uncheck the Automatically Place

Pluses option.

134

If you want to add your own symbols, just use

Text Area objects. Text Area objects are

discussed in Chapter 4.

Dissolving Reactions

To dissolve a built reaction, just select the

arrow the reaction is defined by with a

selection tool, then select the Dissolve

Reactions menu item in the Reaction menu.

Cleaning Reactions

To clean a reaction, perform the following

1. Define the reaction implicitly or explicitly

using the instructions in the previous

2. Select the arrow shape of the reaction you

would like to clean using the selection

3. Press the Clean menu item in the

Reaction menu to clean it.

The reaction arrow will be horizontally

leveled and resized to its text adhering to the

Text Buffer visual specification. Then the

reaction arrow and constituent molecules will

be aligned according to their vertical centers

and distributed horizontally with a buffer

space. The entire reaction is then centered

horizontally. If the reaction is too wide for the

document, the reactants and arrow are then

stacked above the products so that both

groups are mutually centered as shown in

Figure 7.1.

Figure 7.1: A wide reaction that has been stacked.

The settings for determining how reactions

are laid out can be set in the Preferences

Reactions tab as shown in Figure 7.2.

Figure 7.2: Reaction Visual Specifications

You can adjust the double line spacing for

equilibrium arrows, decide whether or not

pluses should be automatically drawn, set the

text buffer for conditions text and the buffer

between constituent reaction objects. You can

also set the default settings for arrowheads.

ChemDoodle can clean multiple reactions at

the same time, but currently can only properly

clean discrete reactions. Cleaning complex

reaction schemes with a given molecule

defined in several different reactions may not

produce desired results.

Figure 7.3: Edit Reaction Window

Reactants

Tray

Text Formatting Tools Reaction Condition Text Areas

136

Products

ChemDoodle understands several

spectroscopy and spectrometry techniques.

These spectra can be loaded and edited to

create graphics.

spectra within ChemDoodle. It covers the

• What types of spectra are supported.

• How to load spectra.

• How to save spectra.

• How to simulate spectra.

• How to edit spectra.

Inserting Spectra

Spectra can be read in from the JCAMP-DX

format which is the standard defined by

IUPAC. The currently supported JCAMP

formats are for nuclear magnetic resonance

spectroscopy (NMR), infrared spectroscopy

(IR), mass spectrometry (MS) and chemical

To insert spectra from JCAMP files, perform

1. Select the Open... menu item in the File

2. In the file chooser that appears, change

the format filter on the bottom to IUPAC

JCAMP-DX.

3. Find the JCAMP file on your computer

and select it with the file chooser.

137

4. Press the Open button at the bottom-right

of the file chooser to load the spectrum.

The spectrum will be loaded and displayed in

the center of a new document.

Spectra Types

Both continuous and discontinuous spectra

are supported. An example of NMR input is

shown in Figure 8.1. An example of IR input

is shown in Figure 8.2. An example of MS

input is shown in figure 8.3.

Figure 8.1: An NMR spectrum loaded from a

JCAMP file.

Figure 8.2: An IR spectrum loaded from a JCAMP

Figure 8.3: An MS spectrum loaded from a

JCAMP file.

Uninterpretable Spectra

There are many different ways to represent

JCAMP data. Therefore, ChemDoodle may

not be able to understand a JCAMP file. If

ChemDoodle was not able to interpret any

spectra from the JCAMP file, you will see the

message shown in Figure 8.4. Please send us

the JCAMP file if you see this issue so that

we may improve our compatibility with the

format.

Figure 8.4: ChemDoodle could not understand the

spectrum in the JCAMP file.

Saving Spectra

ChemDoodle can output spectra in the

following formats:

1. ChemDoodle Documents {.icl, .icxml}

2. IUPAC JCAMP-DX {.jdx, .dx}

Be very careful when overwriting spectra to

formats other than the ChemDoodle

Document. ChemDoodle only reads and

writes the information that is relevant to the

display of its graphics, and other data will be

lost. If saving 3rd party spectra files for any

reason, always save them as a new file.

138

Simulating Spectra

ChemDoodle can simulate spectra for various

techniques. Currently the following

techniques are implemented:

• 1 H Nuclear Magnetic Resonance

Spectroscopy

• 13 C Nuclear Magnetic Resonance

• Mass Spectrum Parent Peak

To simulate spectra, perform the following

• Select a the chemical structure you would

like to simulate a spectrum for using the

• In the Spectrum menu, hover over the

Generate submenu to view available

techniques.

• Click on the technique you would like to

use.

The generated spectrum will then appear on

the Doodle Board. Some very intense

simulations may take a few seconds to

Editing Spectra

Moving Spectra

To move spectra, use a selection tool, either

spectrum so an open hand mouse cursor

appears and the two spectrum anchor

points are drawn as shown in Figure 8.5.

the spectrum.

Figure 8.5: Hovering over the spectrum will

display its anchor points.

Resizing Spectra

To resize spectra, use a selection tool, either

points are drawn as shown in Figure 8.5.

two anchor points so that anchor point is

filled in with an amber color.

spectrum.

Removing Spectra

Spectra can be removed in a number of ways.

139

pointer over the spectrum so an open hand

mouse cursor appears and the two spectrum

8.5. Then press the backspace or delete key.

pointer over the spectrum so the two

spectrum anchor points are drawn. Then

click with the mouse.

• Select the spectrum using any of the

selection tools. Then press the delete or

backspace key.

Expanding the Perspective

Expanding the spectrum will fit the entire

range and domain of the plot to the display

rectangle. Perform the following steps.

1. Use the selection tools to select any

number of spectra.

2. Click on the Expand Perspective menu

item in the Spectrum menu.

All selected spectra will have their

perspectives expanded.

Editing the Perspective

Editing the perspective will allow you to

modify how the plot fits in the viewing

rectangle and will also allow you to edit the

axes and title. These functions are presented

in the Spectrum Edit window as shown in

Figure 8.8.

To change the plot domain, click and drag the

sliders presented directly under the spectrum.

The sliders display, from left to right, the

minimum domain cutoff, the magnitude of the

domain, and the maximum domain cutoff.

You can also change the plot domain by

clicking and dragging on the main spectrum

panel. Click on the placement where you

would like the domain to begin, then drag to

where you would like the domain to end and

elease the mouse. A dotted grey line will

display while dragging to show you the new

domain. Additionally, holding the shift key

while dragging on the spectrum will translate

the domain of the spectrum.

To change the range scale, click and drag the

vertical slider directly to the right of the

spectrum. You can also change the range scale

by using the mouse scroll gesture on the main

spectrum panel. Scroll up to increase the

range scale and scroll down to decrease the

range scale.

To expand the perspective, double-click on

the main spectrum panel.

Changing the Title

To change the title of the spectrum, in the

Spectrum Edit window shown in Figure 8.8,

click on the Title text field located at the

bottom-left and type in the desired title.

Changing the Axes

There are several options for editing the axes.

X-axis options are presented in the X Axis

section of the Spectrum Edit window shown

in Figure 8.8. You can choose to show or hide

it by clicking the Show check box. You can

choose whether to flip the domain or not by

clicking the Flip check box. You can adjust

the increments for the major and minor tick

spacings using the Major Tick Spacing and

Minor Tick Spacing drop down selections.

The values in the drop down selections are

exponents for base 10. You can change the

title of the X-axis by clicking on the Unit text

field and typing the desired title.

Y-axis options are presented in the Y Axis

it by clicking the Show check box. The

Baseline Bump check box will positively

offset the plot by a small value. You can

140

adjust the increment for the major tick

spacing using the Tick Spacing drop down

selection. The values in the drop down

selection are exponents for base 10. You can

change the title of the Y-axis by clicking on

the Unit text field and typing the desired title.

Showing Grids

Grids can be displayed by performing the

1. Hover the spectrum to display the grid

over.

2. Right-click on the spectrum and select the

Format Spectrum... menu item.

3. Scroll down to the Grid section and select

the Show Grid checkbox.

The color and thickness of the grid lines can

also be set in this format window. A grid

appears as shown in Figure 8.6.

Figure 8.6: A grid is displayed over a spectrum.

Showing Integration Lines

Integration lines can be displayed by

1. Hover the spectrum to display the

integration line over.

3. Scroll down to the Integration Line

section and select the Show for NMR

Spectra checkbox.

Field

X Axis

Options

The color and thickness of the integration line

can also be set in this format window. While

intended for NMR spectra, integration lines

can be added to any plot if desired. An

integration line appears as shown in Figure

8.7.

Figure 8.7: An integration line is calculated over

an NMR multiplet.

Domain Sliders

Main Spectrum Panel

141

Figure 8.8: The Spectrum Edit Window

Range

Slider

Y Axis

Chapter 9: Visual

Specifications

All graphics in ChemDoodle are fully

customizable. Visual specifications for the

graphics can be defined for the entire

document, groups of objects or individual

ChemDoodle document settings and visual

specifications. It covers the following topics:

• What are document settings, visual

specifications and style sheets.

• How to create and install custom Chemical

Document Settings files.

• Which graphic specifications can be

customized.

• How to customize the graphics of your

figures.

Document Settings

Document settings are the variables that

determine how graphics are rendered in a

document. They are also called visual

specifications when referring to an individual

object. All together, they form the document’s

style sheet.

Style Sheets

Style sheets can be named when creating

formatted documents. The creation of

formatted documents is discussed in Chapter

1.

In addition to creating or conforming

ChemDoodle documents to the preset style

142

sheets, you can create your style sheets in

ChemDoodle Document Settings files that can

be used later. In the Preferences window,

under the Visuals tab, under the Page tab,

there is a Create Chemical Document

Settings File button at the bottom of the

options. Just perform the following steps to

create a new ChemDoodle Document Settings

file with your completed style sheet:

1. Go through the all of the tabs under the

Visuals tab in the Preferences window

and set all of the values in the options to

the preferred values.

2. Click on the Create Chemical Document

Settings File button in the Preferences

Page tab.

3. A new window will appear. Type in the

name of the ChemDoodle Document

Settings file.

4. Choose three fonts to cascade through.

This is important because different

operating systems have different font sets

and you may have selected a font not

accessible on another operating system if

you want to use it on that operating

system. Serif and SansSerif will always be

defined on all operating systems, so select

those fonts in the third option as wild

cards.

5. Press the Ok button to save the Chemical

Document Settings file.

All Chemical Document Settings files are

saved to the presets folder in the

ChemDoodleSettings folder located in your

folder. Any functions for using ChemDoodle

Document Settings files or for conforming

documents will now list the new style sheet.

If you want to use Chemical Document

Settings files provided by other users of

ChemDoodle, just copy their file into the

presets folder in the ChemDoodleSettings

standard Documents folder. If you have

ChemDoodle open while copying the file,

close and restart it. They copied style sheet

will then be accessible in ChemDoodle.

When you globally change the visual

specifications for a document, ChemDoodle

will ask you if you would like the changed

settings to become the new default settings.

There are two cases when this happens:

1. After opening the Preferences window and

changing visual specifications.

2. After conforming a document using the

Conform Document... menu item in the

Edit menu.

Just click Yes to set the changed settings as

the default settings. Now when a new

document is opened, the current default

settings will be used to define the graphics.

Alternatively, you may answer No to the

question, and later, if you decide to indeed

use the current document settings as the

default document settings, then select the

Save Document Settings... menu item in the

Restore the Original Default Document

Settings

To restore the original default document

settings, open the Preferences window and

click the Restore Defaults button at the

bottom of the window. Then close the

window and select Yes when asked to set the

current settings as the new default settings.

143

Individual Settings

Setting Types

All visual specifications provided in

ChemDoodle are listed in the Preferences

window under the Visuals tab as shown in

Figure 9.1.

Figure 9.1: Visual Specifications

Each visual specification consists of a title to

the left and a component to the right. These

components include:

• On/Off Choices - Click the check box to

choose whether the specification is used or

not. For example, the following check box

will enable or disable the Clear Bond

Overlaps visual specification.

• Single Option Choices - Choose one of the

options from a group exclusively to define

it as the value to use for the specification.

For example one option can be chosen from

the following group set to determine the

value for the Covalent Style specification.

• Number Sliders - Define a number value

by clicking and dragging the slider or by

explicitly typing the value in the text field.

Some number components will be

associated with a dimension drop down

selection to easily set values in other units,

such as centimeters instead of pixels. For

example, slide the slider or type a value into

the text box of the following number

component to define the value for the Bond

Line Thickness specification.

NOTE: Some number components define

angles, and an angle swivel will be

provided instead of a slider. Click and drag

to the angle you want on the swivel to set

the angle.

• Color Buttons - Click on color buttons and

use the color selection window that appears

to select a new color. For example, the

following color button will determine bond

line color.

All objects drawn after changing the visual

specifications in the Preferences window will

conform to the new specifications. All visual

specifications are listed in the following

sections.

Page

144

Background - A color button for the

background color of the document.

Dimensions

Page Size - A specialized component for

setting the page size. Set the width and height

by typing in the text boxes or select a

standard size from the drop down selections.

The button to the left of the text fields will

swap the width and height.

Ångströms / Bond Length - A number slider

for setting the ratio between Ångströms and

the Bond Length specification in pixels. This

specification is useful when finding covalent

bonds and when reading in files with

Ångström coordinates.

Margins

Top - Type in the value for the top page

margin.

Left - Type in the value for the left page

Bottom - Type in the value for the bottom

page margin.

Right - Type in the value for the right page

Text - A color button for the text color of atom

labels.

Buffer Space - A number slider to set the

amount of whitespace between atom text and

the bonds connected to that atom.

Vertical Alignment - A number slider to

control the baseline for rendering text relative

to the center of the atom.

Token Stacking - A single option choice to set

whether atom labels will stack all tokens,

stack only the second token or will never

stack tokens.

Stack Lone/Terminal - An on/off choice to set

whether lone and terminal atoms will stack

their label tokens.

Horizontal Spacing - A number slider to set

the horizontal whitespace between each label

token.

Vertical Spacing - A number slider to set the

vertical whitespace between each label token.

Subscript Reduction - A number slider to set

the size of subscript font relative to the atom

label font.

Subscripts Shift - A number slider to set the

magnitude of the offset from the atom label

font baseline to draw subscripts from.

Superscript Reduction - A number slider to set

the size of superscript font relative to the

atom label font.

Superscript Shift - A number slider to set the

font ascent to draw superscripts from.

Add as - A single option choice to determine

if Hydrogens are added as text to labels or as

atoms with bonds attached.

Add to Carbons - A single option choice to set

how Hydrogens add to Carbons; Hydrogens

can always add to Carbons, can only add to

unsaturated Carbons or will never add to

Carbons.

145

Show Implicit Hydrogens - An on/off choice

to set whether implicit hydrogens are

automatically rendered or not.

Carbons

Display Carbon Labels - A single option

choice to set if Carbon labels display always,

only on lone and hidden Carbons, only on

hidden Carbons, or never show.

Hidden Carbon Angle - An angle number

slider for setting the hidden Carbon angle.

The hidden Carbon angle is the deviation

from 180° between bonds on a Carbon atom

that only has 2 bonds attached to it.

Show Terminal Labels - An on/off choice to

set whether terminal carbon labels are

displayed or not.

Use Circles - An on/off choice for controlling

if element labels are rendered as text or as

circles.

Coloring - A single option choice for

determining whether user chosen colors, CPK

colors, Jmol colors, or PyMOL colors are

used for element labels.

Radius Convention - A single option choice to

control if circles are rendered with a constant

radius, the atomic radius of their element, the

covalent radius of their element or the van der

Waals radius of their element.

Constant Radius - A number slider to set the

constant radius to render element atom circles

with.

Border Width - A number slider to set the

width of the circle outlines when atoms are

rendered as circles.

Fill/Text - A color button for the text color of

attribute labels and graphics.

Logistics

Allowed Distance - A number slider to control

the maximum distance an attribute can be

translated away from the object it defines.

Font Size Reduction - A number slider to

control the font size reduction of attribute text

from its defined font. This is so attribute text

is smaller than the text of the object is

associated with.

Surround with a Circle - An on/off choice to

set whether charges are rendered with a circle

around them.

Diameter - A number slider to set the

diameter of rendered electrons.

Separation - A number slider to set the

separation distance between electrons or

electrons and charges in paired attributes such

as electron pairs and radical cation symbols.

Fill - A color button for the bond line color.

Use Gradient - An on/off choice for rendering

bonds with a gradient between the constituent

atom colors.

146

Split Color - An on/off choice for rendering

bonds that will split the bond color between

the constituent atom colors.

Bond Length - A number slider to define the

optimal length for bonds. This affects

anything that depends on bond length

including drawing bonds and cleaning

Bond Line Thickness - A number slider to

define the width of bond lines.

Bold Bond Thickness - A number slider to

define the width of bold bonds.

Wedge Thickness - A number slider to define

the width of the wide end of wedge bonds.

Unsaturated Spacing (Absolute) - A number

slider to define the spacing between bond

lines in higher order bonds.

Unsaturated Spacing (Relative) - A number

lines in higher order bonds, but relative to the

length of the bond.

Clip Angle - An angle number slider to define

the angle at which non-symmetrical double

bonds will clip the second bond line.

Hash Width - A number slider to define the

width of hashes in bonds rendered with a

hash.

Hash Spacing - A number slider to define the

width the spacing between hashes in bonds

rendered with a hash.

Hash Offset - A number slider to define the

translation from the origin of hashes in bonds

Arrow Length - A number slider to define the

arrowhead length of covalent bonds.

Arrow Angle - An angle number slider to

define the arrowhead angle of covalent bonds.

Wavy Length - A number slider to define the

amplitude of wavy bonds.

Zigzag Length - A number slider to define the

amplitude of zigzag bonds.

Stroke

Style - A drop down selection to set the

default bond stroke style.

Texture - A number slider for setting the

magnitude of texture in stroke styles. For

instance, a higher number will cause Bristle

strokes to look more bristled.

Bond Ends - A single option choice to set how

bond ends are rendered; with no cap, a round

cap or a square cap.

Join Bond Connections - An on/off choice to

define whether the rendering engine will

merge bonds end together for more aesthetic

graphics.

Double Bond Asymmetry - A single option

choice to set when double bonds will be

rendered asymmetrically; always, when

between 2 Carbons, only in rings or never.

Heteroatom Retraction - An on/off choice that

defines whether asymmetric double bonds

will retract the second line from an atom or

not based on that atom being a heteroatom.

Terminal Retraction - An on/off choice that

defines whether terminal double bonds will

retract the second line from a terminal atom

or not.

Unsaturated Spacing - A single option choice

for setting whether unsaturated bonds are

147

rendered with an absolute spacing or with a

relative spacing between bond lines.

Changing this specification will place the

corresponding visual specification in the

Settings section.

Even Hashes - An on/off choice to determine

if the Hash Width and Hash Offset

specifications only affect Bold Dashed and

Recessed bonds.

Clear Bond Overlaps - An on/off choice to

determine if an overlapped bond will erase

the section of overlap.

Overlap Clear Width - A number slider to

define the length of the bond that is erased

when overlapped.

Covalent Style - A single option choice to set

if covalent bonds are rendered as Polar

Covalent bonds with a slash in the stroke, or

as Coordinate Covalent bonds.

Indent Arrow Bond - An on/off choice to set if

covalent bond arrowheads are indented.

Fused

Favor Aromatics - An on/off choice to force

double bonds in fused systems to face

aromatic rings over non-aromatic rings.

Double Bond Orientation - A single option

choice to determine if double bonds in fused

ring systems will face larger rings or smaller

Aromatics

Use Circles - An on/off choice to render

aromatics with a circle instead of in Kekulé

Circle Radius - An number slider to define the

diameter of the aromatic circle relative to the

dimensions of the ring.

Layout

Double Line Spacing - A number slider to

define the spacing between the lines in

equilibrium arrows.

Automatically Place Plusses - An on off

choice to set whether reactions automatically

place plusses between constituent reactants

and products.

Text Buffer - A number slider to define the

buffer between the text set as the reaction

conditions and the ends of the associated

arrow when the text is centered. This value

times 2 will determine the default length that

arrows without associated text are cleaned to

when cleaning reactions.

Constituent Buffer - A number slider to define

the spacing between reaction constituents

Arrowheads

Length - A number slider to define the

arrowhead length of arrow shapes.

Angle - An angle number slider to define the

arrowhead angle of arrow shapes.

Borders and Lines - A color button for the

lines and borders of shapes.

Fill - A color button for the fill color of

shapes.

Text - A color button for the text color of

148

Shapes Add - A single option choice to set

whether shapes are drawn in front of atoms or

behind atoms.

Strokes

Thickness - A number slider to define the

width of solid strokes in shapes.

width of hashes in shapes rendered with a

width the spacing between hashes in shapes

translation from the origin of hashes in shapes

Shadows

Translation - A number slider to define the

distance from the shape the shadow should be

rendered.

angle in relation to the shape to place the

shadow.

Opacity - A number slider to define the

transparency of shadows.

Wideness - A number slider to define the

width of bracket lips relative to the standard

size.

Length Multiplier - A number slider to define

the default extent of orbitals in bond lengths.

So if the length multiplier is 1, then all

orbitals placed will have a length of 1 bond

length.

Stroke Shaded Lobes - An on/off choice to set

whether shaded lobes in orbitals will also be

outlined.

Paths

Close - An on/off choice to set if paths are

closed by default.

Rounded Arc Width - A number slider to

define the width of the corner arcs in rounded

rectangles.

Rounded Arc Height - A number slider to

define the height of the corner arcs in rounded

Show Major Ticks - An on/off choice to set if

major ticks are shown in rulers.

Close - An on/off choice to set if minor ticks

are shown in rulers.

Unit - A drop down selection to set the default

units of ruler objects.

Spectra

Plots - A color button for the spectrum plots.

Grids - A color button for the spectrum grids.

Integration Lines - A color button for the

spectrum integration lines.

Plot Strokes

width of solid strokes in spectrum plots.

149

Hash - An on/off choice to render spectrum

plots with a hashed stroke.

width of hashes in spectrum plots rendered

with a hash.

width the spacing between hashes in spectrum

plots rendered with a hash.

translation from the origin of hashes in

spectrum plots rendered with a hash.

Grids

Show - A on/off switch to set whether

spectrum grids are shown by default.

Thickness - A number slider to define the line

thickness of spectrum grids.

Integration Lines

spectrum integration lines are shown by

default.

thickness of spectrum integration lines.

Editing Visual Specifications

For Single Objects

To edit the visual specifications of a single

object, perform the following steps:

1. Switch to a selection tool and make sure

the current selection is empty.

2. Hover the mouse pointer over the object

of which the visual specifications are to

be changed.

3. Right-click on the object and select the

Format Object... menu item or doubleclick

on the object.

4. Change the visual specifications in the

window that appears. You will see the

graphics update in real-time on the

5. Click the Done button in the window to

set the changes.

You can also press the Cancel button to

cancel all changes.

For a Group of Objects

To edit the visual specifications of a group of

objects, perform the following steps:

1. Switch to a selection tool.

2. Select all of the content of which the

visual specifications are to be changed.

3. Open the Preferences window and click

on the Visuals tab.

4. Change all the visual specifications in the

Visuals tab to your preference. You will

see the graphics update in real-time on the

5. Click the Done button in the Preferences

window to set the changes.

Current Style Sheet

To conform a group of objects to the current

style sheet, perform the following steps:

3. Press the Conform to Document

Settings menu item in the Content menu.

All content will conform to the visual

specifications defined in the document’s style

sheet. This function will also change fonts

150

and scale structures to match the defined bond

Different Style Sheet

To conform the entire document to a different

1. Press the Conform Document... menu

2. In the window that appears, choose the

style sheet you prefer from the drop down

3. You will be asked if you would like to

conform atom text by changing fonts;

choose Yes or No.

4. If the bond length has changed, you will

be asked if you would like the structures

to be scaled to match the new value;

The entire document will now conform to

your choice of style sheet.

3D Graphics

ChemDoodle is a tool for generating 2D

graphics. However, ChemDoodle handles 3D

input and you can create orthographic 2D

scenes of your 3D data. That being said, with

all of the bond types and atom labels

showing, the figure may not be very aesthetic.

To create better looking 2D orthographic

scenes of your 3D data, perform the following

suggestions.

• Change all bonds to plain single bonds, and

include double bonds if necessary.

• Change the visual specifications to show all

atoms as circles instead of as text labels.

• Change the visual specifications to render

atoms with their Jmol colors.

• Increase the bond line width visual

specification.

bonds with a gradient between their

• Increase the bond overlap buffer visual

specification to clearly show bond overlaps.

We have provided a sample style sheet to

quickly create 2D orthographic scenes from

3D data that can be accessed when creating a

formatted document or conforming a given

document as is described in the previous

section called Orthographic 3D Scene.

Bond Stroke Styles

ChemDoodle provides several bond stroke

styles to casually style your structures for

presentations, posters and more casual media.

To change bond stroke styles, select the bonds

to be changed with a selection tool and use

the Stroke toolbar.

The default bond line stroke width is 1.2

pixels. This is not sufficient to see some

stroke styles and the value will need to be

increased. Other stroke styles, such as the

Brush style, will not display well for really

short bonds and structures rendered with

those styles should be expanded.

The following bond stroke styles are currently

provided:

• Basic -

• Bristle -

151

• Brush -

• Calligraphy -

• Charcoal -

• Scribble -

• Wobble -

Advanced Document

Rendering

The graphics defined by ChemDoodle are

always exact and based on very precise

coordinates. However, the screen that you use

to display ChemDoodle and bitmap images

that are output will need to define the

graphics in a much less precise resolution.

Algorithms have been developed to minimize

the perception of this loss of resolution and

ChemDoodle provides full access to control

how the graphics are rendered. Note that

scalable vector graphics are also exact and

based on precise coordinates and are therefore

resolution-less. The following settings will

only affect the display of graphics on your

computer monitor and the output of bitmap

graphics; scalable vector graphics will not be

Advanced document rendering settings can be

defined in the Preferences window under the

Advanced tab.

Anti-Aliasing

Anti-aliasing controls whether or not the

geometry rendering methods will attempt to

reduce aliasing artifacts along the edges of

shapes. Anti-aliasing is enabled by default.

A typical antialiasing algorithm works by

blending the existing colors of the pixels

along the boundary of a shape with the

requested fill paint according to the estimated

partial pixel coverage of the shape. This

function reduce the appearance of jagged

edges. Figure 9.2 is a structure rendered

without anti-aliasing enabled, while Figure

9.3 is a structure rendered with anti-aliasing

enabled.

Figure 9.2: Anti-aliasing is disabled.

Figure 9.3: Anti-aliasing is enabled.

152

Font Fractional Metrics

Font fractional metrics controls whether the

positioning of individual character glyphs

takes into account the sub-pixel accuracy of

the scaled character advances of the font or

whether such advance vectors are rounded to

an integer number of whole device pixels.

This hint only recommends how much

accuracy should be used to position the

glyphs and does not specify or recommend

whether or not the actual rasterization or pixel

bounds of the glyph should be modified to

match. Font fractional metrics are disabled by

default to produce better graphics for bitmap

images and for the computer screen. In

ChemDoodle, this property does not affect

printing. Since printing is usually with a high

resolution device, ChemDoodle will always

enable font fractional metrics for printer

rendering.

Rendering text to a low resolution device like

a screen will necessarily involve a number of

rounding operations as the high quality and

very precise definition of the shape and

metrics of the character glyphs must be

matched to discrete device pixels. Ideally the

positioning of glyphs during text layout

would be calculated by scaling the design

metrics in the font according to the point size,

but then the scaled advance width will not

necessarily be an integer number of pixels. If

the glyphs are positioned with sub-pixel

accuracy according to these scaled design

metrics then the rasterization would ideally

need to be adjusted for each possible subpixel

Unfortunately, scaling each glyph customized

to its exact subpixel origin during text layout

would be prohibitively expensive so a

simplified system based on integer device

positions is typically used to lay out the text.

The rasterization of the glyph and the scaled

advance width are both adjusted together to

yield text that looks good at device resolution

and has consistent integer pixel distances

between glyphs that help the glyphs look

uniformly and consistently spaced and

readable.

This process of rounding advance widths for

rasterized glyphs to integer distances means

that the character density and the overall

length of a string of text will be different from

the theoretical design measurements due to

the accumulation of a series of small

differences in the adjusted widths of each

glyph. The specific differences will be

different for each glyph, some being wider

and some being narrower than their

theoretical design measurements. Thus the

overall difference in character density and

length will vary by a number of factors

including the font, the specific device

resolution being targeted, and the glyphs

chosen to represent the string being rendered.

As a result, rendering the same string at

multiple device resolutions can yield widely

varying metrics for whole strings.

When font fractional metrics are enabled, the

true font design metrics are scaled by the

153

point size and used for layout with sub-pixel

accuracy. The average density of glyphs and

total length of a long string of characters will

therefore more closely match the theoretical

design of the font, but readability may be

affected since individual pairs of characters

may not always appear to be consistent

distances apart depending on how the subpixel

accumulation of the glyph origins

meshes with the device pixel grid. Enabling

this hint may be desirable when text layout is

being performed that must be consistent

across a wide variety of output resolutions.

Specifically, this hint may be desirable in

situations where the layout of text is being

previewed on a low resolution device like a

screen for output that will eventually be

rendered on a high resolution printer or

typesetting device.

When disabled, the scaled design metrics are

rounded or adjusted to integer distances for

layout. The distances between any specific

pair of glyphs will be more uniform on the

device, but the density and total length of

long strings may no longer match the

theoretical intentions of the font designer.

Disabling this hint will typically produce

more readable results on low resolution

devices like computer monitors.

Dithering

Dithering controls how closely to

approximate a color when storing into a

destination with limited color resolution.

Dithering is enabled by default

Some rendering destinations may support a

limited number of color choices which may

not be able to accurately represent the full

spectrum of colors that can result during

rendering operations. For such a destination,

dithering controls whether rendering is done

with a flat solid fill of a single pixel value

which is the closest supported color to what

was requested, or whether shapes will be

filled with a pattern of colors which combine

to better approximate that color.

Rendering Algorithm

This setting provides a high level

recommendation as to whether to bias

algorithm choices more for speed or quality

when evaluating tradeoffs. This hint could be

consulted for any rendering or image

manipulation operation, but decisions will

usually honor other, more specific settings in

preference to this setting. The rendering

algorithm is set to Quality by default.

Alpha Interpolation Algorithm

The alpha interpolation setting is a general

setting that provides a high level

recommendation as to whether to bias alpha

blending algorithm choices more for speed or

quality when evaluating tradeoffs. The alpha

interpolation algorithm is set to Quality by

This setting controls the choice of alpha

blending calculations that sacrifice some

precision to use fast lookup tables or lower

precision SIMD instructions. This hint could

also control whether or not the color and

alpha values are converted into a linear color

space during the calculations for a more linear

visual effect at the expense of additional perpixel

calculations.

Color Rendering Algorithm

The color rendering algorithm controls the

accuracy of approximation and conversion

when storing colors into a destination image

or surface. The color rendering algorithm is

set to Quality by default.

When a rendering or image manipulation

operation produces a color value that must be

stored into a destination, it must first convert

154

that color into a form suitable for storing into

the destination image or surface. Minimally,

the color components must be converted to bit

representations and ordered in the correct

order or an index into a color lookup table

must be chosen before the data can be stored

into the destination memory. Without this

minimal conversion, the data in the

destination would likely represent random,

incorrect or possibly even unsupported

values. Algorithms to quickly convert the

results of rendering operations into the color

format of most common destinations are well

known and fairly optimal to execute.

Simply performing the most basic color

format conversion to store colors into a

destination can potentially ignore a difference

in the calibration of the color space of the

source and destination or other factors such as

the linearity of the gamma correction. Unless

the source and destination color space are

identical, to correctly perform a rendering

operation with the most care taken for the

accuracy of the colors being represented, the

source colors should be converted to a device

independent color space and the results then

converted back to the destination color space.

Furthermore, if calculations such as the

blending of multiple source colors are to be

performed during the rendering operation,

greater visual clarity can be achieved if the

intermediate device independent color space

is chosen to have a linear relationship

between the values being calculated and the

perception of the human eye to the response

curves of the output device.

Stroke Control

Stroke control defines whether a rendering

implementation should or is allowed to

modify the geometry of rendered shapes for

various purposes. Stroke control is set to Best

Compromise by default.

Some implementations may be able to use an

optimized platform rendering library which

may be faster than traditional software

rendering algorithms on a given platform, but

which may also not support floating point

coordinates. Some implementations may also

have sophisticated algorithms which perturb

the coordinates of a path so that wide lines

appear more uniform in width and spacing.

If an implementation performs any type of

modification or "normalization" of a path, it

should never move the coordinates by more

than half a pixel in any direction.

When stroke control is set to Normalize,

geometry will be altered to improve

uniformity or spacing of lines and overall

aesthetics. The compromise is that geometry

will be offset to fit to the pixel resolution of

the rendering device. A consequence is that

lines that are parallel may not appear exactly

parallel, such as in double bonds.

When stroke control is set to Pure, geometry

will be left unmodified and rendered with

sub-pixel accuracy. There will be noticeable

lightness and bolding in straight lines that are

vertical or horizontal.

Figure 9.5 shows a rectangle and structure

displayed with stroke control set to Pure,

while Figure 9.6 shows the same objects with

stroke control set to Normalize.

Figure 9.5: A structure and rectangle rendered

with stroke control set to Pure. Notice the bolding

and blurring of the horizontal and vertical lines.

155

Figure 9.6: A structure and rectangle rendered

with stroke control set to Normalize. Notice that

parallel lines are not preserved.

For even better graphics, a third option is

provided called Best Compromise. This

option will use pure stroke control for all

chemical structures. All other shapes will first

be analyzed for vertical and horizontal lines,

and any found will be rendered with

normalized stroke control while the rest of the

graphics will be rendered with pure stroke

Image Scaling

Image scaling controls how image pixels are

filtered or resampled during an image

rendering operation. This will have noticeable

affects on images that are not rendered in

their natural scale. The image scaling

algorithm is set to Progressive Bilinear by

Implicitly images are defined to provide color

samples at integer coordinate locations. When

images are rendered upright with no scaling

onto a destination, the choice of which image

pixels map to which device pixels is obvious

and the samples at the integer coordinate

locations in the image are transferred to the

pixels at the corresponding integer locations

on the device pixel grid one for one. When

images are rendered in a scaled, rotated, or

otherwise transformed coordinate system,

then the mapping of device pixel coordinates

back to the image can raise the question of

what color sample to use for the continuous

coordinates that lie between the integer

locations of the provided image samples.

Interpolation algorithms define functions

which provide a color sample for any

continuous coordinate in an image based on

the color samples at the surrounding integer

coordinates.

Progressive Bilinear is better than Bicubic

which is better than Bilinear which is better

than Nearest-Neighbor at producing

reasonable graphics of stretched or shrunken

bitmap images. The better the algorithm used,

the worse the runtime will get.

Chapter 10:

Sharing

Information

ChemDoodle has advanced functions for

interacting with other applications on your

computer. This is essential for inputting

graphics into word processors or for

transferring chemical data into modeling

applications.

ChemDoodle’s system clipboard capabilities.

It covers the following topics:

• Introducing the system clipboard.

• How to copy data and graphics from

ChemDoodle into other applications.

• How to copy data and graphics from other

applications into ChemDoodle.

• What types of data can be transferred.

• What image formats are supported.

• How to save images.

• How to insert images.

• How to take advantage of round trip editing.

The System Clipboard

The system clipboard is a construct of the

operating system that contains data for

sharing between applications. Only one

application can place data on the system

clipboard at a time. Other applications can

then see that data and load it. This system

forms the basis for copy and paste

157

functionality. ChemDoodle will place a wide

range of chemical and graphic data on the

system clipboard as well as associate that data

with the correct MIME types for other

applications to use.

MIME Types

A MIME type is an identifier to define the

data it is associated with. For example, a

structure can be represented in MDL

MOLFile format. The MDL MOLFile format

is a plain text format and can be associated

with the MIME type, text/plain. However, this

is a very generic description and other

applications will only recognize it as plain

text, rather than as a chemical structure.

Therefore a different MIME type is associated

with this data, chemical/x-mdl-molfile, to

define it as a structure in the MDL MOLFile

format. In this manner, other applications will

recognize this data as a chemical.

ChemDoodle follows the MIME standards put

forth by the Chemical MIME Project (http://

www.ch.ic.ac.uk/chemime/). This should be

regarded as the standard, however, many

chemical software developers do not follow

these rules, thereby causing issues when

transferring data between chemical

Additionally, since many items can be present

on the system clipboard at once, applications

may paste a certain data type by default that

may not be the data you want to paste. For

instance, Microsoft Word can paste both text

data types and image data types. If both are

present on the system clipboard, Microsoft

Word will automatically select the text data

type when pasting, even if you wanted the

image to be pasted. There can even be

different image types, confusing the situation

Therefore, ChemDoodle allows you to define

how data and which data is placed on the

system clipboard to work with the

applications that you use.

Clipboard Settings

ChemDoodle can transfer data to almost any

application that has been created. But it is

impossible for ChemDoodle to determine

which data should be transferred. Therefore,

you need to set the appropriate Copy Settings

to make sure any ambiguities are resolved

with the application you are pasting to. Copy

Settings can be set in the Preferences

window under the Advanced tab as shown in

Figure 10.1. These settings will allow you to

explicitly control what data ChemDoodle will

transfer to other applications.

Figure 10.1: Copy Settings

There are three main types of data that may

be transferred:

• Text Types - Contains a line or lines of text

that will be interpretable by other

applications. Some chemical formats are

also listed here to be pasted as text into

other applications. All text data will be

interpreted as text by other applications and

158

any chemical significance will be lost. Only

one text data type will be placed on the

system clipboard at a time.

• Image Types - This group contains both

bitmap and vector images. Bitmap images

are not scalable in resolution. Vector images

are much more versatile and will remain

crisp and clear regardless of resizing or

transformation. Bitmap and vector images

are discussed in detail in the next section.

• Chemical Types - Chemical types include

structure information. Only chemical

programs will see these.

Therefore, to work with other applications,

first decide what type of data you would like

to transfer and what types of data the other

application accepts. Then set the appropriate

copy settings to continue.

Scalable Vector Graphics

There are two types of images, bitmap and

vector. Bitmap images are traditional images

and define a rectangle of pixels and their

colors, while vector images define drawing

instructions for recreating it. When resizing,

the bitmap will become blurry, pixelated and

lose its quality while the vector image will

remain crisp and clear. Figure 10.2 shows a

bitmap image of a structure, while Figure

10.3 shows a vector image of the same

structure. Both were created by ChemDoodle.

Try zooming in on both images using your

PDF reader and you can see the difference in

quality for yourself.

Figure 10.2: A Bitmap Image

Figure 10.3: A Vector Image

Bitmap images will suffer from this issue

with any change of resolution, including

printing to a printer. Because of this, we

recommend you insert vector images into

your documents. The only downside to using

vector graphics is that some programs may

not support them. ChemDoodle compatibility

with 3rd party applications is discussed in

Appendix C.

If you must use a bitmap image, then

ChemDoodle provides high resolution options

(such as scaling and DPI control) for a few

bitmap formats as discussed in the Image

Output Options section later in this chapter.

159

Copying Data to Other

Applications

Using the Copy Function

To copy data from ChemDoodle into other

applications, perform the following steps:

1. Determine which data you would like to

transfer and the types of data that the

other application can accept and configure

the copy settings in the Preferences

window under the Advanced tab

accordingly.

2. Select the objects on the Doodle Board

that you would like to copy using the

content selection tools.

3. Click on the Copy menu item in the Edit

menu or press its menu accelerator

keyboard shortcut which is ctrl-C

(command-C on Mac OS X).

4. Use the paste function present in the other

application to paste the content. If the

other application has a Paste Special...

function, you may use that to specify

which data type to paste.

Using the Copy As Function

The copy as functions are preset shortcuts for

placing certain data forms on the system

clipboard without changing the data types to

be copied in the Advanced tab of the

Preferences window.

Just select the content in the document to be

copied and then select one of the menu items

in the Copy As... submenu of the Edit menu.

The most popular data types are supported.

These functions will place both text and

chemical data on the system clipboard for

maximum compatibility with 3rd party

applications. No image data will be placed on

the system clipboard.

Pasting Data from Other

To paste data from other applications into

ChemDoodle, perform the following steps:

1. Use the copy function present in the other

2. Click on the Paste menu item in the Edit

keyboard shortcut which is ctrl-V

(command-V on Mac OS X) to paste the

highest priority data to the Doodle Board.

Where Content is Pasted

The pasted content will be located according

to the following rules:

1. If your mouse pointer is hovering over the

document, the center of the pasted content

will be located at the mouse pointer.

2. If the mouse pointer is not hovering over

the document, and the lasso is active, then

the pasted content will appear to the

bottom-right of the lassoed content.

3. If the mouse pointer is not hovering over

the document and the lasso is inactive,

then the pasted content will appear at the

Inappropriate

You have already flagged this document. Thank you, for helping us keep this platform clean. The editors will have a look at it as soon as possible.

Mail this publication

Delete template.

Are you sure you want to delete your template?

DOWNLOAD ePAPER

This ePaper is currently not available for download. You can find similar magazines on this topic below under ‘Recommendations’.

Save as template?

document download and read ad-free!

No annoying ads and unlimited download of all publications

7 days free trial!*

Help & Support
tuxbrain.com
ooomacros.org
nubuntu.org
Terms of service
Privacy policy
Cookie policy
Cookie settings

Choose your language

Main languages

Further languages

Bahasa Indonesia

Performing this action will revert the following features to their default settings:

Hooray! Your file is uploaded and ready to be published.

Saved successfully!

Ooh no, something went wrong!

blockbion.blogg.se

#Chemdoodle help formal charge plus#

#chemdoodle help formal charge professional#.

To complete this exercise, try drawing both of the representations of the sulfate ion shown above. Note that the overall charge on this ion is -2. This is done by setting up the data and a few styles for the Canvas. The center-left number defines the multiple count. You can create renderings of Lewis Dot Structures with the ChemDoodle Web Components.

The bottom-right number defines the repeat count. The top-right number defines the charge amount. Pressing the up and down arrows will increment and decrement the values at these positions. Drag diagonally to the opposite corner of the rectangle defined by the brackets and release the mouse, In this mode, up and down arrows will be displayed at various positions on the bracket. ZINC ensuring physical similarity of six properties (molecular weight, formal charge. To show the formal charge on an atom in ChemDoodle, use the + or - tools that have.

For example, in the drawing of the sulfate ion (SO42-) shown on the left, each oxygen atoms is assigned a formal charge of minus one and the sulfur atom is assigned a formal charge of plus two. Add a structure to the canvas and then add brackets around it by pressing the mouse down where the first corner of the bracket will start. DUD-E is designed to help test docking algorithms by providing. Formal charges may be associated with atoms in Lewis structures. To place brackets a structure, use the bracket from the toolbar.

To show the charge on an ion in ChemDoodle, use the bracket tool described below. Check out ChemDoodle 3D Get both now for only 15 ChemDoodle 3D 3D Chemical Graphics, Animations and Modeling Professional Quality, Affordable Prices Trusted by thousands of institutions in over 100 countries Chemistry World Review (Win/Mac/Linux v7) Dr. In a Lewis structure, the charge on an ion is placed as a superscript on surrounding square brackets, as shown for the sulfate ion in the drawing to the right. The overall ion charge is a property of an ion as a hole and is not associated with a particular atom.

One can calculate the formal charges for any given atom with the help of the following formula: F. These charges help in knowing if the given structure of the molecule is stable or not. To show the formal charge on an atom in ChemDoodle, use the + or - tools that have been described previously. Formal charge is the individual electric charges on the atoms in a given polyatomic molecule. For example, in the drawing of the sulfate ion (SO_4^2-) shown on the left, each oxygen atoms is assigned a formal charge of minus one and the sulfur atom is assigned a formal charge of plus two. Transcribed image text: Formal charges may be associated with atoms in Lewis structures.

Tutorial > Lewis Dot Structures

You can create renderings of Lewis Dot Structures with the ChemDoodle Web Components . This is done by setting up the data and a few styles for the Canvas .

For atoms, it is important to show lone pairs by setting the Atom.numLonePair variable as shown in the following examples. The sketcher also has tools to allow the drawing of lone pairs. The lone pairs will automatically be placed in the optimal positions. You can change how lone pairs appear with the following styles:

atoms_lonePairDistance_2D - This is the distance between the lone pair and the atom.
atoms_lonePairSpread_2D - This is the distance between the electrons in the pair.
atoms_lonePairDiameter_2D - This is the diameter of the dots that represent the electrons.

Additionally, you will want to display all carbon labels by setting the atoms_displayAllCarbonLabels_2D style to true, and by turning off the display of implicit hydrogens by setting the atoms_implicitHydrogens_2D style to false.

Neither the MDL MOLFile or Daylight SMILES formats support lone pairs, so validation must be done programmatically by accessing the Molecule data structure, by visual analysis, or by using the ChemDoodle JSON format .

For bonds, set the bonds_lewisStyle_2D style to true for traditional Lewis Dot Structures. You may also want to set up the atom coordinates longer bond lengths to clearly show off multiple bonds and at 90° angles.

You can also use the ChemDoodle.iChemLabs.createLewisDot() function from iChemLabs Cloud services . This function creates a Molecule that represents the input molecule as a Lewis Dot Structure using 90° angles and appropriately place lone pairs to satisfy the octet rule (charges will need to be present on the input molecule).

Just a simple one to start, Neon with 8 electrons:

Chloroform, showing carbon labels and with implicit hydrogens off:

Hydrogen sulfate anion:

Get your work done with our popular desktop software.

ChemDoodle 2D

ChemDoodle 3D

IMAGES

Solved Add formal charges. Consider the incomplete
Solved Add formal charges to each resonance form of HCNO.
Solved Draw I with three lone pairs and add formal charges,
Draw I with three lone pairs and add formal
Solved Add formal charges to each resonance form of HCNO.
OneClass: Add formal charges to a,b and c ..and which structure would be favored? Add formal

VIDEO

ChemDoodle 2D to 3D Coordinates demo
Calculation of Oxidation no of Central Metal Atom in a Complex
How To Add Formal Attire to Rush ID Pictures
ChemDoodle Shorts: Functional Groups
ChemDoodle Mechanism Arrows Only Question
Cheryl Tweedy & Kimberley Walsh with Frank Skinner (P1)

COMMENTS

What Is the Formal Charge on Nitrogen in NO3?
The formal charge of nitrogen in the compound NO3 is plus 1. The whole nitrate ion carries a total charge of minus 1 when combining the charges of the one nitrogen atom and three oxygen atoms.
What Is the Charge on a Sulfate Ion?
The formal charge of the sulfate ion, which has the molecular formula (SO4)2-, is -2. Ions that have a negative charge are called anions, and positively charged ions are called cations.
What Is the Ionic Charge of SO4?
The ionic charge of SO4 is -2. Ionic, or formal, charge is not an actual charge of the chemical, but rather an estimate of electron distribution within a molecule or ion, based on a simplified model.
Answer ChemDoodle Sketcher Questions
Click the down arrow next to the attributes button. options for changing the attributes of an atom · Click increase charge to increase the charge, or decrease
Chemdoodle help formal charge
To show the formal charge on an atom in ChemDoodle, use the + or - tools that have been described previously. This sum does equal the overall
ChemDoodle 3D Chemoodie Sketcher. Formal charge, ion
To show the formal charge on an atom in ChemDoodle, use the + or -tools ... add brackets around it by pressing the mouse down where the first
ACHIEVE: How to add formal charges and find “missing” molecules
ACHIEVE: How to add formal charges and find “missing” molecules. 3.4K views · 2 years ago ...more. Roxi Hulet. 17.2K. Subscribe.
ChemDoodle Shorts: Lewis Dot Structures
Comments. thumbnail-image. Add a comment... 4 ... Lewis Structures, Introduction, Formal Charge, Molecular Geometry, Resonance, Polar or Nonpolar.
ChemDoodle Shorts: Lewis Dot Structures
In this #ChemDoodle Short, we will be discussing #Lewis dot structures. The focus is on drawing Lewis structures for simple molecules.
ChemDoodle v5.0 User Guide
Adding Charges ................................ 84 . Incrementing and ... ChemDoodle guess formal charges for a .
Demos > 2D Sketcher
Charges - After a charge sign has been selected, hover an atom and click the mouse to add or subtract from that atom's charge amount. Lone Pairs - After a
Chemdoodle help formal charge
You can create renderings of Lewis Dot Structures with the ChemDoodle Web Components. chemdoodle help formal charge. The bottom-right number
Tutorial > Lewis Dot Structures
(charges will need to be present on the input molecule). Examples. Just a
ChemDoodle 3D Version History
The major new feature is the ability to add charges, radicals