
ACD/ChemSketch Version 11.0 for Microsoft Windows Tutorial Drawing Chemical Structures and Graphical Images Advanced Chemistry Development, Inc. Copyright © 1997–2007 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 © 2007 Microsoft Corporation. All rights reserved. IBM is a registered trademark of International Business Machines Corporation Copyright © IBM Corporation 1994, 2007. 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 © 2007 Adobe Systems Incorporated. All rights reserved. Camtasia is a registered trademark of TechSmith Corporation, and Camtasia Studio is a trademark of TechSmith Corporation Copyright © 1999–2007 TechSmith Corporation. All rights reserved. All the other trademarks mentioned within this tutorial are the property of their respective owners. All trademarks are acknowledged. Information in this document is subject to change without notice and is provided “as is” with no warranty. Advanced Chemistry Development, Inc., makes no warranty of any kind with regard to this material, including, but not limited to, the implied warranties of merchantability and fitness for a particular purpose. Advanced Chemistry Development, Inc., shall not be liable for errors contained herein or for any direct, indirect, special, incidental, or consequential damages in connection with the use of this material. 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 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 Double and Triple Bonds ........................................................................................ 6 2.2.3 Deleting Atoms Individually .................................................................................... 6 2.2.4 The Undo Command .............................................................................................. 7 2.2.5 Polymers................................................................................................................. 7 2.2.6 Pseudo Atoms ........................................................................................................ 7 2.2.7 Changing the Atom................................................................................................. 8 2.2.8 Using the Draw Continuous Tool............................................................................ 9 2.2.9 Using Mouse Drag.................................................................................................. 9 2.2.10 “Cleaning” the Structure.......................................................................................... 9 2.2.11 Editing Atom Labels.............................................................................................. 10 2.2.12 Draw Chains Tool ................................................................................................. 11 2.3 Clearing the Screen...........................................................................................12 2.4 Using ACD/Dictionary—Commercial version only!............................................ 12 2.5 Flipping Structures ............................................................................................14 2.6 Output................................................................................................................15 2.6.1 Saving a ChemSketch (.SK2) File........................................................................ 15 2.6.2 Saving a Structure to a MDL Molfile..................................................................... 16 2.6.3 Printing.................................................................................................................. 16 2.6.4 Embedding the Structure in a Document ............................................................. 17 3. Drawing More Complex Structures ........................................................ 18 3.1 Objectives..........................................................................................................18 3.2 Using the Table of Radicals ..............................................................................18 3.3 Using Ring Structures .......................................................................................19 3.4 Deleting Atoms and Fragments.........................................................................20 3.4.1 Deleting Several Atoms Simultaneously .............................................................. 20 3.5 Replacing Atoms ...............................................................................................21 ACD/ChemSketch Tutorial i Table of Contents 3.6 Setting Double and Triple Bonds.......................................................................22 3.7 Setting Charges and Defining Anions and Cations ........................................... 22 3.8 Markush Bonds .................................................................................................24 3.8.1 Markush Bond with Added or Removed Fragment .............................................. 25 3.9 Generating Stereo Descriptors..........................................................................25 3.10 Drawing Coordination Bonds ..........................................................................26 3.11 Delocalized Charges and Curves ................................................................... 29 3.12 More Bond Types............................................................................................31 3.13 Changing Atom Properties..............................................................................33 4. Advanced Structures, SMILES and InChI Notations, Reaction Schemes35 4.1 Objectives..........................................................................................................35 4.2 2D-Optimization.................................................................................................35 4.2.1 Creating the Structure of Cyclic Alkanes.............................................................. 35 4.2.2 Creating the Structure of a Cyclic Peptide ........................................................... 36 4.3 SMILES Notations.............................................................................................38 4.3.1 Generating SMILES Notations ............................................................................. 38 4.3.2 Generating Structures from SMILES Notations.................................................... 38 4.4 InChI Notations..................................................................................................39 4.4.1 Generating InChI Notations .................................................................................. 40 4.4.2 Generating Structures from InChI Notations ........................................................ 41 4.5 3D-Optimization.................................................................................................41 4.5.1 Creating Structure of Bicyclo[2.2.2]octane ..........................................................
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