ChemDraw 19.1 User Guide ChemDraw: User Guide Table of Contents Recent Additions vii Chapter 1: Introduction 1 About this Guide 1 Chapter 2: Getting Started 4 About ChemDraw Tutorials 4 ChemDraw User Interface 4 Toolbars 5 Documents 6 Chapter 3: Page Layout 15 The Drawing Area 15 The Document Type 15 Printing 17 Saving Page Setup Settings 18 35mm Slide Boundary Guides 18 Viewing Drawings 19 Tables 21 Chapter 4: Preferences and Settings 25 Setting Preferences 25 Customizing Toolbars 31 Document and Object Settings 32 Customizing Hotkeys 42 Working with Color 44 Document Settings 50 Chapter 5: Shortcuts and Hotkeys 56 Atom Hotkeys 56 Bond Hotkeys 59 Generic Hotkeys (tool switching hotkeys) 61 © Copyright 1998-2020 PerkinElmer Informatics, Inc. All rights reserved. i ChemDraw: User Guide Modified Hotkeys 62 Drawing Reactions Using Hotkeys 62 Shortcuts 63 Nicknames 67 Chapter 6: Basic Drawings 70 Bonds 70 Atoms 75 Captions 76 Drawing Rings 85 Chains 89 Objects 90 Clean Up Structure 109 Checking Structures 110 Chemical Warnings 111 Chapter 7: BioDraw (Professional Level only) 113 BioDraw Templates 113 Customizable Objects 116 Chapter 8: Drawing Monomer Sequences 122 Drawing Amino Acid Sequences 125 Drawing RNA Sequences 133 Replacing Monomers 135 Copying Sequence(s) as HELM String 135 Pasting HELM Strings 136 Copying a Sequence as HELM (Natural Analog) 137 Nonlinear Sequences (Multi-line Sequences) 139 Basic Sequence Operations 140 Monomer Editors 147 ChemDraw Shared Monomers 152 © Copyright 1998-2020 PerkinElmer Informatics, Inc. All rights reserved. ii ChemDraw: User Guide Chapter 9: Advanced Drawing Techniques 160 Coloring Objects 160 Labels 161 Attachment Points 164 Atom Numbering 167 Structure Perspective 168 Mass Fragmentation 169 Drawing Reactions 171 Stoichiometry Grid 177 Templates 181 Defining Nicknames 183 ChemScript 186 Chapter 10: Struct=Name (Professional Level) 188 Struct>Name 188 Name>Struct 194 Adding Structures to a Dictionary 197 Dictionary of FDA Approved Drugs 197 Chapter 11: Chemistry Features 198 Structure Analysis 198 Stereochemistry 200 Chemical Properties 204 Chemical Annotations 211 3D Viewing 215 TLC 218 ChemNMR (Professional Level) 223 Chapter 12: ChemDraw/Excel and CombiChem 231 Setting Up ChemDraw/Excel 231 Importing tables 231 © Copyright 1998-2020 PerkinElmer Informatics, Inc. All rights reserved. iii ChemDraw: User Guide Importing hit lists 232 Exporting tables 232 Synchronizing Tables 233 Adding structures 234 Searching 235 R-Group analysis 236 Working with Structures 237 ChemDraw/Excel Functions 239 Chemical Properties 253 General Preferences 261 CombiChem 262 Chapter 13: ChemScript 271 Why use ChemScript? 271 How ChemScript works 272 Getting Started 272 Editing Scripts 273 Introducing the ChemScript API 274 Tutorials 275 Useful References 278 Chapter 14: Query Structures 280 Search Limitations 280 Generic Labels 280 Atom Properties 283 Bond Properties 291 Element Lists 294 Polymers 295 Alternative Groups 301 Anonymous Alternative Groups 308 © Copyright 1998-2020 PerkinElmer Informatics, Inc. All rights reserved. iv ChemDraw: User Guide Expand Generic Structures 309 Expand Generic Structure To SDF 312 Atom-to-Atom Mapping 315 Stereochemical Symbols 318 3D Properties 318 Export Compatibility 319 Chapter 15: Sharing Information 324 The Clipboard 324 Transferring Objects 327 Embedding Objects 328 Exporting 329 Importing 330 Transferring Across Platforms 334 Understanding ChemDraw Cloud 334 Chapter 16: Chemical Interpretation 346 Database Conventions 346 Chapter 17: Property Calculations 359 Chapter 18: ChemDraw Add-ins 362 Add-in Manager 362 ChemACX.com Structure from CAS Registry Number Add-in 367 ChemACX Explorer Add-in 368 Dynamic Add-ins 379 PubChem GHS LCSS Add-in 381 Creating a ChemDraw Add-in 383 ChemDraw Add-in Tutorials 386 Creating a Remote Add-in 394 Adding a Remote Add-in 395 OAuth Based Authorization Workflow in ChemDraw Add-ins 396 © Copyright 1998-2020 PerkinElmer Informatics, Inc. All rights reserved. v ChemDraw: User Guide Chapter 19: ChemDraw Web Resources 400 400 User’s Guide 400 Technical Support 400 ChemDraw Web Resources 401 Querying SciFinder® with ChemDraw 402 Querying Reaxys® with ChemDraw 404 Chapter 20: Tutorials 408 Tutorial 1: Drawing a Structure 408 Tutorial 2: Drawing rings 409 Tutorial 3: Fischer projections 411 Tutorial 4: Perspective Drawings 414 Tutorial 5: Newman projections 418 Tutorial 6: Stereochemistry 421 Tutorial 7: Templates 424 © Copyright 1998-2020 PerkinElmer Informatics, Inc. All rights reserved. vi ChemDraw: User Guide Recent Additions Querying Reaxys® with ChemDraw. Reaxys is a web-based chemical search engine designed for synthetic and medicinal chemists. The Reaxys data- base includes chemical properties, structures, reactions and experimental data. Using the Search Reaxys func- tionality, you can now search the Reaxys database for query structures drawn in ChemDraw. If your subscription is through a university or institution, you can use a proxy server to connect you to Reaxys®. For more details, see "Querying Reaxys® with ChemDraw " on page 404. Import/Export Reaction Data Files. ChemDraw now supports importing and exporting Reaction Data Files. You can choose to import .rd or .rdf (v2000 and v3000) files. Ring Fill Colors. Using the Ring Fill Colors option, you can now fill different ring structures with colors of your choice. The ring color is propagated when atom labels and nicknames in generic structures are expanded. For more details, see "Ring Fill Colors" on page 46. Atom Hotkey to add atom label CF3. You can now use the hotkey Shift+f to add the atom label CF3. For more information on Atom Hotkeys see, "Atom Hotkeys" on page 56. Add-ins Toolbar. The Search toolbar has now been renamed to Add-ins toolbar. The Scifinder® and Reaxys® search buttons are now located on this toolbar. For more information, see "The Add-ins Toolbar" on page 379. Dynamic Add-ins. ChemDraw now supports dynamic add-ins. A dynamic add-in behaves like a normal add-in, with the addition that a button will be dynamically added to the Add-ins toolbar when the add-in is successfully loaded. For more information, see "Dynamic Add-ins" on page 379. PubChem GHS LCSS Add-ins. You can use the PubChem GHS LCSS add-in to search for the selected structure and its safety data in PubChem from the ChemDraw interface. You can also copy the GHS Hazard Statement and the Precautionary Statement Codes to the clipboard. For more information, see "PubChem GHS LCSS Add-in" on page 381. Accessing remote add-ins. © Copyright 1998-2020 PerkinElmer Informatics, Inc. All rights reserved. vii ChemDraw: User Guide You can now access add-ins deployed on remote sites. Deploying add-ins on remote sites accessible by ChemDraw makes the central management of such add-ins much more convenient. For more details, see "Creating a Remote Add-in" on page 394. Expand Generic Structure To SDF. You can now export multiple structures from an annotated combinatorial structure with the Expand Generic Structure to SDF option. For details, see "Expand Generic Structure To SDF" on page 312. Parameterized brackets. The paired brackets are now parameterized i.e. you can specify the label or repeat count and/or the molecular weight. When the molecular weight is specified, the specified molecular weight overrides the molecular weight of the molecules inside the brackets. For more information, see "Paired Brackets" on page 97, "Molecular Weight Override and Derived Calculations" on page 199 and "Converting Unspecified Bracket Type to Parameterized Bracket" on page 299. Support for native Pistoia Alliance format. ChemDraw now supports the native Pistoia Alliance format for the monomer database for both read and write oper- ations. For details, see "ChemDraw Shared Monomers" on page 152. ChemDraw Shared Monomers. ChemDraw can be used as a full featured monomer editing and curation tool. Monomers can be downloaded from web, network or local locations, and written anywhere the user has write permission. Monomers can be entered de-novo, or imported via CDXML files or from JSON libraries. For more information, see "ChemDraw Shared Monomers" on page 152. Toggle Aromatic Display. Toggle Aromatic Display option lets you change an aromatic structure from Alternating double/single bond to Aromatic circle and vice versa. You can now define the way aromatic structures are displayed when you open a file of non nat- ive chemical format or paste as SMILES. For more information, see "Toggle Aromatic Display" on page 88. © Copyright 1998-2020 PerkinElmer Informatics, Inc. All rights reserved. viii ChemDraw: User Guide Introduction Designed for scientists, students, and scientific authors, ChemDraw is a powerful, yet easy-to use, tool for producing chemical and biological drawings. You can create your own drawings or use those provided in the library of available templates. Technical Support The online menu link Technical Support opens the Technical Support Web page. Here you can find desktop support resources, including the PerkinElmer Informatics Knowledge Base, product downloads, FAQ, and documentation. To reach the PerkinElmer Informatics Technical Support Web page: 1. Navigate to Online>Browse PerkinElmer Technical Support. The Technical Support Web page opens. 2. Click Desktop Support. About this Guide This guide describes the features in ChemDraw. Some tasks described in this guide must be performed in conjunction with other software. For example, instructions for ChemDraw/Excel describe tasks that require Microsoft Excel. For