ChemDraw 16.0 User Guide ChemDraw 16.0 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 12 The Drawing Area 12 The Document Type 12 Printing 14 Saving Page Setup Settings 15 35mm Slide Boundary Guides 15 Viewing Drawings 16 Tables 18 Chapter 4: Preferences and Settings 22 Setting Preferences 22 Customizing Toolbars 26 Document and Object Settings 26 Customizing Hotkeys 36 Working with Color 39 Document Settings 42 Chapter 5: Shortcuts and Hotkeys 48 Atom Keys 48 Bond Hotkeys 49 Function Hotkeys 50 © Copyright 1998-2016 PerkinElmer Informatics Inc., All rights reserved. i ChemDraw 16.0 Shortcuts 51 Nicknames 55 Chapter 6: Basic Drawings 57 Bonds 57 Atoms 62 Captions 63 Drawing Rings 72 Chains 75 Objects 76 Clean Up Structure 93 Checking Structures 95 Chemical Warnings 95 Chapter 7: BioDraw (Professional Level only) 98 BioDraw Templates 98 Customizable Objects 101 Chapter 8: Drawing Biopolymers 107 Biopolymer Editor 108 Protecting Groups 109 Pasting Sequences 110 Expanding Sequences 112 Contracting Labels 112 Modifying Sequence Residues 113 Merging Sidechains with Residue 114 Hybrid Biopolymers 117 IUPAC Codes 118 Disulfide Bridges 122 Lactam Bridges 123 Chapter 9: Advanced Drawing Techniques 124 © Copyright 1998-2016 PerkinElmer Informatics Inc., All rights reserved. ii ChemDraw 16.0 Coloring Objects 124 Labels 125 Attachment Points 128 Atom Numbering 130 Structure Perspective 132 Mass Fragmentation 132 Drawing Reactions 135 Stoichiometry Grid 141 Templates 144 Defining Nicknames 146 ChemScript 149 Chapter 10: Struct=Name (Professional Level) 151 Struct>Name 151 Name>Struct 155 Adding Structures to a Dictionary 157 Dictionary of FDA Approved Drugs 157 Chapter 11: Chemistry Features 158 Structure Analysis 158 ChemFinder hotlink 159 Stereochemistry 160 Chemical Properties 164 Chemical Annotations 171 3D Viewing 175 TLC 177 ChemNMR (Professional Level) 182 Chapter 12: ChemDraw/Excel and CombiChem 190 Setting Up ChemDraw/Excel 190 Importing tables 190 © Copyright 1998-2016 PerkinElmer Informatics Inc., All rights reserved. iii ChemDraw 16.0 Importing hit lists 191 Exporting tables 191 Synchronizing Tables 192 Adding structures 193 Searching 194 R-Group analysis 195 Working with Structures 196 ChemDraw/Excel Functions 198 Chemical Properties 212 General Preferences 220 CombiChem 222 Chapter 13: 230 Why use ChemScript? 230 How ChemScript works 230 Getting Started 231 Editing Scripts 232 Introducing the ChemScript API 233 Tutorials 234 Useful References 237 Chapter 14: Query Structures 238 Search Limitations 238 Generic Labels 238 Atom Properties 241 Bond Properties 249 Element Lists 252 Polymers 253 Alternative Groups 258 Anonymous Alternative Groups 264 © Copyright 1998-2016 PerkinElmer Informatics Inc., All rights reserved. iv ChemDraw 16.0 Expand Generic Structures 265 Atom-to-Atom Mapping 267 Stereochemical Symbols 270 3D Properties 271 Export Compatibility 272 Chapter 15: Sharing Information 277 The Clipboard 277 Transferring Objects 280 Embedding Objects 281 Exporting 281 Importing 282 Transferring Across Platforms 286 Understanding ChemDraw Cloud 286 Chapter 16: Chemical Interpretation 300 Database Conventions 300 Chapter 17: Property Calculations 313 Chapter 18: ChemDraw Web Resources 316 Registering Online 316 User’s Guide 316 Technical Support 316 Querying SciFinder® with ChemDraw (Professional Level) 318 Chapter 19: Tutorials 321 Tutorial 1: Drawing a Structure 321 Tutorial 2: Drawing rings 322 Tutorial 3: Fischer projections 324 Tutorial 4: Perspective Drawings 327 Tutorial 5: Newman projections 331 Tutorial 6: Stereochemistry 334 © Copyright 1998-2016 PerkinElmer Informatics Inc., All rights reserved. v ChemDraw 16.0 Tutorial 7: Templates 337 © Copyright 1998-2016 PerkinElmer Informatics Inc., All rights reserved. vi ChemDraw 16.0 Recent Additions Windows 10 (32 bit and 64 bit), Microsoft Office 365, and Mac OS X 10.10.x and 10.11.x (32 bit and 64 bit). ChemDraw strives to be a vital and preferred tool for illustrating chemical and biological concepts. Compatibility with the latest operating systems and tools is an essential part of that. Having the ChemDraw Active-X control functional with the latest browsers on both Windows and Mac platforms is part of this process as well. Enhanced Retrosynthesis Tool. Using the Enhanced Retrosynthesis tool, you can now analyze how a molecule might have been constructed. For details, see ""Enhanced Retrosynthesis tool" on page 134". ChemDraw Cloud. ChemDraw is now available without any installation in ChemDraw Cloud. ChemDraw Desktop and ChemDraw Cloud can share files via upload and download. For details, see "Understanding ChemDraw Cloud" on page 286 Attach Data feature enhancement. You can now specify a single character tag while attaching data to an object. These tags will be displayed along with objects. For details, see ""Attached Data" on page 283". Stereoflag Configuration Options. You can choose to display one general stereoflag label for the molecule (instead of stereoflag labels in individual ste- reo-centers) when opening MDL format files. For details see, "Configuration options for stereoflag" on page 23. You can now save the Enhanced Stereochemistry settings when saving to the SKC format. For details, see "Con- figuration options for stereoflag" on page 23. ChemDraw E-Notebook. ChemDraw E-Notebook is a cloud-based tool supporting design and recording of chemistry experiments. ChemDraw E-Notebook and desktop ChemDraw can share ChemDraw documents. Note: ChemDraw E-Notebook is not yet available at the time of ChemOffice 16.0 release but will be available soon. For details, see "What is ChemDraw E-Notebook?" on page 298. Recent Additions vii ChemDraw 16.0 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 and screens. Menu items appear in bold. For example, to open a new drawing template: 1. Go to File>Open Templates>Amino Acids. This step asks you to select the File menu, select Open Templates (in the File menu), and then select Amino Acids (in the Open Templates sub menu). Notes, Tips, and Cautions The guide uses particular icons for various types of information: Note: Notes highlight important information. Tip: Tips supply useful, specific, “nice to know”, information, supplemental to the main text. Caution: Cautions indicate important information that, if ignored, may lead to data loss ,or other serious problems. Additional Information These resources are available to help you get started with ChemDraw: Online Help In ChemDraw, press <F1> or navigate to Help>Contents. Chapter 1: Introduction 1 of 338 ChemDraw 16.0 Tool Tips This is the name or a short description of a tool. To view a tool tip, point to a tool. A longer description of the tool tip is available in the status bar. Status Bar See the lower left corner of the ChemDraw window for useful information, as shown below. Figure 1.1: Status bar displaying information about solid bond. Serial Number and Technical Support For more information on obtaining serial numbers and registration codes, see the online Services Web site. Technical support is available to registered users through the Internet and our Technical Support department.When contacting Technical Support, always provide the serial number of your ChemOffice application. Our Technical Support Web pages contain answers to frequently asked questions (FAQs) and other information. To access our Technical Support in ChemDraw, navigate to Online>Browse PerkinElmerTechnical Support. If you are unable to find a solution on the Web site, follow these steps before you contact Technical Support: 1. Check the system requirements for the software. 2. Read and follow suggestions outlined in "Troubleshooting" on page 3 . 3. If your attempts to resolve a problem fail, contact Technical support. Before you call: Try to reproduce the problem before contacting us. If you can reproduce the problem, please record the exact steps. Record the exact wording of any error messages that appear. Record your attempts to correct the problem. Additional sources of ChemOffice information are: ChemDraw online Help The PerkinElmer Informatics Web site. PerkinElmer Informatics Services. Chapter 1: Introduction 2 of 338 ChemDraw 16.0 Troubleshooting This section describes steps you can take that affect the overall