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Pcmodel V 9.0 PCMODEL V 9.0 Molecular Modeling Software for Windows Operating System Apple Macintosh OS Linux and Unix Serena Software Box 3076 Bloomington, IN 47402-3076 (812)-333-0823 © 1993-2004 Serena Software. All rights reserved. First Edition June 1998 Second Edition June 1999 Third Edition January 2001 Fourth Edition April 2002 Fifth Edition August 2003 Sixth Edition August 2004 Trademarks IBM and IBM PC are registered trademarks of International Business Machines Inc. Windows is a registered trademark of the Microsoft Corporation. Alchemy and Sybyl are registered trademarks of Tripos Associates, Inc. Chem-3D is a registered trademark of Cambridge Scientific Computing, Inc. ISIS is a trademark of MDL Information Systems, Inc. 2 License Agreement Serena Software provides these programs and licenses their use in your teaching and research. You assume responsibility for the use of the program to achieve your intended results. You may: 1. Use the programs on any machine or machines in your possession. 2. Copy the programs and source code into any machine readable form for backup or modification purposes in support of your use of the programs. 3. Modify the programs and source code or merge them into another program for your use. (Any portion of these programs or source code or merged programs resulting will continue to be subject to the terms and conditions of this agreement.) You may not: 1. Give copies of these programs to anyone else, unless you destroy all copies you have in any form. 2. Sell copies of these programs. 3. Use the programs on a network, unless others are prevented from accessing the programs. This license is effective until terminated. You may terminate it at any time by destroying the programs and source code together with all copies, modifications and merged portions in any form. These programs are provided "AS IS" and without warranty of any kind, either expressed or implied. The entire risk as to the quality and performance of the programs is with the user. Serena Software does not warrant the operation of the programs will be uninterrupted or error free. If Serena Software is unable to deliver a copy of the programs that is satisfactory, you may obtain a full refund by returning all the program materials and documentation within 30 days of date of delivery. These programs are intended for use in chemical research and teaching. Serena Software will not be liable in any event to you for any damages, including any lost profits, lost savings or other incidental or consequential damages arising out of the use or inability to use these programs even if Serena Software has been advised of the possibility of such damages, or for claim by any other party. 3 Table of Contents Table of Contents ....................................................................................................................................... 4 Chapter 1. Overview.................................................................................................................................. 9 1.1 Introduction ..................................................................................................................................... 9 1.2 Changes in Version 7........................................................................................................................ 9 1.3 Changes in Version 7.5 ..................................................................................................................... 9 1.40 Changes in Version 8.0 ................................................................................................................. 10 1.41 Changes in Version 8.5 ................................................................................................................. 10 1.42 Changes in Version 9.0 ................................................................................................................. 10 1.5 History............................................................................................................................................ 10 1.6 The PCMODEL Window............................................................................................................... 12 1.7 Definitions..................................................................................................................................... 13 1.8 Closing Notes ................................................................................................................................. 13 Chapter 2. Installation.............................................................................................................................. 15 2.1 Windows Installation ...................................................................................................................... 15 2.2 Macintosh Installation..................................................................................................................... 15 2.3 Linux Installation............................................................................................................................ 16 2.4 General Comments ......................................................................................................................... 17 Chapter 3. Quick Summary of PCMODEL Menu Bar Functions .............................................................. 19 Chapter 4. Tutorials................................................................................................................................. 25 4.1 Methylcyclohexane......................................................................................................................... 25 4.1.1 Drawing the Structure .............................................................................................................. 25 4.1.2 Building the Structure .............................................................................................................. 28 4.1.3 Minimizing and Adjusting the Structure................................................................................... 29 4.2 Trans-Decalin ................................................................................................................................ 30 4.3 Special Options............................................................................................................................... 31 4.3.1 Compare .................................................................................................................................. 31 4.3.2 Rotational Energy Barriers ....................................................................................................... 32 4.4 Benzene and a Pi Calculation.......................................................................................................... 32 4.5 Biphenyl and a Pi Calculation ......................................................................................................... 32 4.6 Ferrocene - Using Metals and Coordination .................................................................................... 33 4.7 The Methanol dimer - Hydrogen Bonding and Docking .................................................................. 33 4.8 Substructures - Creation and Manipulation...................................................................................... 34 4.8.1 Building Polystryene using Dummy Atoms.............................................................................. 35 4.9 Diels-Alder Transition State............................................................................................................ 35 Chapter 5. Drawing Tools........................................................................................................................ 38 5.1.1 Select Atom ................................................................................................................................. 38 5.1.2 Select Bond.................................................................................................................................. 38 5.2 Draw............................................................................................................................................... 38 5.3 Build............................................................................................................................................... 39 5.4 Update ............................................................................................................................................ 39 5.5 H/AD.............................................................................................................................................. 39 5.6 Add_B ............................................................................................................................................ 39 5.7 In .................................................................................................................................................... 39 5.8 Out ................................................................................................................................................. 39 5.9 Del.................................................................................................................................................. 40 5.10 Move ............................................................................................................................................ 40 5.11 Rotate Bond.................................................................................................................................
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