ACD/ChemSketch Version 12.0 for Microsoft Windows Tutorial Drawing Chemical Structures and Graphical Images Advanced Chemistry Development, Inc. Copyright © 1997–2010 Advanced Chemistry Development, Inc. All rights reserved. ACD/Labs is a trademark of Advanced Chemistry Development, Inc. Microsoft and Windows are registered trademarks of Microsoft Corporation in the United States and/or other countries Copyright © 2010 Microsoft Corporation. All rights reserved. IBM is a registered trademark of International Business Machines Corporation Copyright © IBM Corporation 1994, 2010. All rights reserved. Adobe, Acrobat, PDF, Portable Document Formats, and associated data structures and operators are either registered trademarks or trademarks of Adobe Systems Incorporated in the United States and/or other countries Copyright © 2010 Adobe Systems Incorporated. All rights reserved. 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Table of Contents Before You Begin ............................................................................................... v Freeware Version ......................................................................................................... v About This Tutorial ....................................................................................................... v Advanced Understanding ......................................................................................................vi Mouse Conventions..................................................................................................... vi For More Information… ...............................................................................................vii How to Contact Us................................................................................................................vii Online Updates .....................................................................................................................vii 1. Basics of ACD/ChemSketch...................................................................... 1 1.1 Objectives............................................................................................................ 1 1.2 Starting ACD/ChemSketch.................................................................................. 1 1.3 Setting File Associations ..................................................................................... 2 1.3.1 Changing File Associations .................................................................................... 2 1.4 Changing Default Directories .............................................................................. 3 1.5 Installing Add-Ons............................................................................................... 3 1.6 Quitting ACD/ChemSketch.................................................................................. 4 2. Drawing Simple Structures ....................................................................... 5 2.1 Objectives............................................................................................................ 5 2.2 Drawing Atoms, Bonds, and Labels .................................................................... 5 2.2.1 Using the Draw Normal Tool .................................................................................. 5 2.2.2 Drawing Double and Triple Bonds.......................................................................... 6 2.2.3 Cancelling Actions .................................................................................................. 6 2.2.4 Deleting Individual Atoms ....................................................................................... 7 2.2.5 Polymers................................................................................................................. 7 2.2.6 Pseudo Atoms ........................................................................................................ 8 2.2.7 Changing the Atom................................................................................................. 9 2.2.8 Using the Draw Continuous Tool.......................................................................... 10 2.2.9 Drawing Bond Between Two Atoms..................................................................... 10 2.2.10 “Cleaning” Structure.............................................................................................. 11 2.2.11 Editing Atom Labels.............................................................................................. 12 2.2.12 Rotating Structural Fragments.............................................................................. 13 2.2.13 Drawing Chains .................................................................................................... 14 2.3 Cleaning the Screen.......................................................................................... 15 2.4 Using ACD/Dictionary........................................................................................ 16 2.5 Flipping Structures ............................................................................................ 17 2.6 Output................................................................................................................ 18 2.6.1 Saving ACD/ChemSketch Document to ChemSketch (.SK2) File....................... 19 2.6.2 Saving Structure to MDL Molfile ........................................................................... 19 2.6.3 Printing ACD/ChemSketch Document.................................................................. 20 2.6.4 Embedding ACD/ChemSketch Structure into Third-Party Document .................. 20 3. Drawing More Complex Structures ........................................................ 22 3.1 Objectives.......................................................................................................... 22 3.2 Using the Table of Radicals .............................................................................. 22 3.3 Using Ring Structures ....................................................................................... 24 3.4 Deleting Atoms and Groups .............................................................................. 25 3.4.1 Deleting Several Atoms Simultaneously .............................................................. 25 ACD/ChemSketch Tutorial i Table of Contents 3.5 Replacing Atoms and Groups ........................................................................... 26 3.6 Setting Double Bonds........................................................................................ 27 3.7 Setting Charges and Defining Anions and Cations ........................................... 28 3.8 Drawing Markush Bonds ................................................................................... 30 3.8.1 Markush Bond with Added or Removed Fragment .............................................. 31 3.9 Generating Stereo Descriptors.......................................................................... 32 3.10 Drawing Coordination Bonds .......................................................................... 33 3.11 Delocalized Charges and Curves ................................................................... 36 3.12 More Bond Types............................................................................................ 39 3.13 Changing Atom Properties.............................................................................. 42 4. Advanced Structures, SMILES and InChI Notations, and Reaction Schemes............................................................................................................ 44 4.1 Objectives.......................................................................................................... 44 4.2 2D-Optimization................................................................................................. 44 4.2.1 Creating the Structure of Cyclic Alkanes.............................................................. 44 4.2.2 Creating the Structure of a Cyclic Peptide ........................................................... 45 4.3 SMILES Notations............................................................................................. 47 4.3.1 Generating SMILES Notations ............................................................................. 47 4.3.2 Generating Structures from SMILES Notations.................................................... 47 4.4 InChI Notations.................................................................................................. 49 4.4.1 Generating InChI Notations .................................................................................. 49 4.4.2 Generating Structures from InChI Notations .......................................................