ChemDraw 19.0 User Guide ChemDraw 19.0 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 45 Document Settings 50 Chapter 5: Shortcuts and Hotkeys 56 Atom Hotkeys 56 Bond Hotkeys 60 Generic Hotkeys (tool switching hotkeys) 61 © Copyright 1998-2019 PerkinElmer Informatics, Inc. All rights reserved. i ChemDraw 19.0 Modified Hotkeys 62 Drawing Reactions Using Hotkeys 63 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 1998-2019 PerkinElmer Informatics, Inc. All rights reserved. ii ChemDraw 19.0 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 180 Defining Nicknames 182 ChemScript 185 Chapter 10: Struct=Name (Professional Level) 187 Struct>Name 187 Name>Struct 193 Adding Structures to a Dictionary 196 Dictionary of FDA Approved Drugs 196 Chapter 11: Chemistry Features 197 Structure Analysis 197 Stereochemistry 199 Chemical Properties 203 Chemical Annotations 210 3D Viewing 214 TLC 217 ChemNMR (Professional Level) 222 Chapter 12: ChemDraw/Excel and CombiChem 230 Setting Up ChemDraw/Excel 230 Importing tables 230 © Copyright 1998-2019 PerkinElmer Informatics, Inc. All rights reserved. iii ChemDraw 19.0 Importing hit lists 231 Exporting tables 231 Synchronizing Tables 232 Adding structures 233 Searching 234 R-Group analysis 235 Working with Structures 236 ChemDraw/Excel Functions 238 Chemical Properties 252 General Preferences 260 CombiChem 261 Chapter 13: ChemScript 270 Why use ChemScript? 270 How ChemScript works 271 Getting Started 271 Editing Scripts 272 Introducing the ChemScript API 273 Tutorials 274 Useful References 277 Chapter 14: Query Structures 279 Search Limitations 279 Generic Labels 279 Atom Properties 282 Bond Properties 290 Element Lists 293 Polymers 294 Alternative Groups 300 Anonymous Alternative Groups 307 © Copyright 1998-2019 PerkinElmer Informatics, Inc. All rights reserved. iv ChemDraw 19.0 Expand Generic Structures 308 Expand Generic Structure To SDF 311 Atom-to-Atom Mapping 313 Stereochemical Symbols 316 3D Properties 317 Export Compatibility 318 Chapter 15: Sharing Information 323 The Clipboard 323 Transferring Objects 326 Embedding Objects 327 Exporting 328 Importing 329 Transferring Across Platforms 333 Understanding ChemDraw Cloud 333 Chapter 16: Chemical Interpretation 345 Database Conventions 345 Chapter 17: Property Calculations 358 Chapter 18: ChemDraw Add-ins 361 Add-in Manager 361 ChemACX.com Structure from CAS Registry Number Add-in 366 ChemACX Explorer Add-in 367 Dynamic Add-ins 378 PubChem GHS LCSS Add-in 380 Creating a ChemDraw Add-in 382 ChemDraw Add-in Tutorials 385 Creating a Remote Add-in 393 Adding a Remote Add-in 394 OAuth Based Authorization Workflow in ChemDraw Add-ins 395 © Copyright 1998-2019 PerkinElmer Informatics, Inc. All rights reserved. v ChemDraw 19.0 Chapter 19: ChemDraw Web Resources 399 399 User’s Guide 399 Technical Support 399 Querying SciFinder® with ChemDraw 400 Querying Reaxys® with ChemDraw 402 Chapter 20: Tutorials 406 Tutorial 1: Drawing a Structure 406 Tutorial 2: Drawing rings 407 Tutorial 3: Fischer projections 409 Tutorial 4: Perspective Drawings 412 Tutorial 5: Newman projections 416 Tutorial 6: Stereochemistry 419 Tutorial 7: Templates 422 © Copyright 1998-2019 PerkinElmer Informatics, Inc. All rights reserved. vi ChemDraw 19.0 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 402. 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 378. 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 378. 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 380. Accessing remote add-ins. 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 393. Expand Generic Structure To SDF. © Copyright 1998-2019 PerkinElmer Informatics, Inc. All rights reserved. vii ChemDraw 19.0 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 311. 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 198 and "Converting Unspecified Bracket Type to Parameterized Bracket" on page 298. 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 1998-2019 PerkinElmer Informatics, Inc. All rights reserved. viii ChemDraw 19.0 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 assistance, consult the Microsoft Excel online help or user’s guide. Conventions used in this Guide This guide uses several basic conventions to help you quickly learn ChemDraw. Instructions Instructions are designed to help you navigate through menus