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ACD/ChemSketchVersion 12.0 for Microsoft Windows

Tutorial

Drawing Chemical Structures and Graphical Images

Advanced Chemistry Development, Inc.Copyright 19972008 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 2008 Microsoft Corporation. All rights reserved. IBM is a registered trademark of International Business Machines Corporation Copyright IBM Corporation 1994, 2008. 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 2008 Adobe Systems Incorporated. All rights reserved. Camtasia is a registered trademark of TechSmith Corporation, and Camtasia Studio is a trademark of TechSmith Corporation Copyright 19992008 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 ContentsBefore You Begin ............................................................................................... vFreeware Version ......................................................................................................... v About This Tutorial ....................................................................................................... vAdvanced Understanding ......................................................................................................vi

Mouse Conventions..................................................................................................... vi For More Information ...............................................................................................viiHow to Contact Us................................................................................................................vii Online Updates .....................................................................................................................vii

1.

Basics of ACD/ChemSketch...................................................................... 11.1 1.2 1.3 1.4 1.5 1.6 Objectives............................................................................................................ 1 Starting ACD/ChemSketch.................................................................................. 1 Setting File Associations ..................................................................................... 2Changing File Associations .................................................................................... 2

1.3.1

Changing Default Directories .............................................................................. 3 Installing Add-ons................................................................................................ 3 Quitting ChemSketch .......................................................................................... 4

2.

Drawing Simple Structures ....................................................................... 52.1 2.2 Objectives............................................................................................................ 5 Drawing Atoms, Bonds, and Labels .................................................................... 5Using the Draw Normal Tool .................................................................................. 5 Double and Triple Bonds ........................................................................................ 6 Deleting Atoms Individually .................................................................................... 6 The Undo Command .............................................................................................. 7 Polymers ................................................................................................................. 7 Pseudo Atoms ........................................................................................................ 7 Changing the Atom ................................................................................................. 8 Using the Draw Continuous Tool............................................................................ 9 Using Mouse Drag .................................................................................................. 9 Cleaning the Structure........................................................................................ 10 Editing Atom Labels.............................................................................................. 10 Draw Chains Tool ................................................................................................. 11

2.2.1 2.2.2 2.2.3 2.2.4 2.2.5 2.2.6 2.2.7 2.2.8 2.2.9 2.2.10 2.2.11 2.2.12

2.3 2.4 2.5 2.6

Clearing the Screen........................................................................................... 12 Using ACD/DictionaryCommercial version only!............................................ 13 Flipping Structures ............................................................................................ 14 Output................................................................................................................ 15Saving a ChemSketch (.SK2) File ........................................................................ 15 Saving a Structure to a MDL Molfile ..................................................................... 16 Printing.................................................................................................................. 16 Embedding the Structure in a Document ............................................................. 17

2.6.1 2.6.2 2.6.3 2.6.4

3.

Drawing More Complex Structures ........................................................ 183.1 3.2 3.3 3.4 3.5 Objectives.......................................................................................................... 18 Using the Table of Radicals .............................................................................. 18 Using Ring Structures ....................................................................................... 19 Deleting Atoms and Fragments......................................................................... 20Deleting Several Atoms Simultaneously .............................................................. 20

3.4.1

Replacing Atoms ............................................................................................... 21

ACD/ChemSketch

Tutorial

i

Table of Contents

3.6 3.7 3.8

Setting Double and Triple Bonds....................................................................... 22 Setting Charges and Defining Anions and Cations ........................................... 22 Markush Bonds ................................................................................................. 24Markush Bond with Added or Removed Fragment .............................................. 25

3.8.1

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 Schemes354.1 4.2 4.3 4.4 4.5 Objectives.......................................................................................................... 35 2D-Optimization................................................................................................. 35Creating the Structure of Cyclic Alkanes.............................................................. 35 Creating the Structure of a Cyclic Peptide ........................................................... 36 Generating SMILES Notations ............................................................................. 38 Generating Structures from SMILES Notations.................................................... 38 Generating InChI Notations .................................................................................. 40 Generating Structures from InChI Notations ........................................................ 41 Creating Structure of Bicyclo[2.2.2]octane ........................................................... 41 Creating the Structure of Triptycene .................................................................... 43 Creating the Structure of Cubane......................................................................... 44 Creating the Structure of Dodecahedrane ([5]Fullerene-C20)............................... 45 Drawing a Reaction Scheme ................................................................................ 47 Labeling a Reaction ...................................................

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