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Tutorial and User's Guide Tutorial and User's Guide WA VEFUNCTION Wavefunction, Inc. 18401 Von Karman Avenue, Suite 370 Irvine, CA 92612 U.S.A. www.wavefun.com Wavefunction, Inc., Japan Branch Office 3-5-2, Kouji-machi, Suite 608 Chiyoda-ku, Tokyo, Japan 102-0083 [email protected] • www.wavefun.com/japan Copyright © 2011 by Wavefunction, Inc. All rights reserved in all countries. No part of this book may be reproduced in any form or by any electronic or mechanical means including information storage and retrieval systems without permission in writing from the publisher, except by a reviewer who may quote brief passages in a review. ISBN978-1-890661-41-4 Printed in the United States of America Acknowledgements The Spartan’10 Tutorial and User’s Guide was prepared by Warren Hehre and Sean Ohlinger, who take both credit for its utility and blame for its limitations and inaccuracies. Several members of Wavefunction contributed significantly, with Philip Klunzinger, Bernard Deppmeier, Andy Driessen and Jeffrey Johnson warranting special mention. As with past manuals, sincere thanks goes to Pamela Ohsan for turning a sloppy manuscript into a finished book. Scope of this Guide This guide provides a general reference for Spartan’10 for Windows, Macintosh and Linux. It is divided into 22 chapters grouped into three sections, along with several appendices. Section I (Introduction, Chapter 1) introduces Spartan as a tool for exploring organic, bioorganic, inorganic and organometallic chemistry by way of molecular mechanics and quantum chemical calculations, together with an array of graphical models for conveying the results of these calculations. The section ends with a brief discussion of new capabilities in Spartan’10 as well as changes and improvements over previous versions. Section II (Getting Started, Chapters 2 to 11) describes the overall operating environment of Spartan, and then provides an extensive set of hands-on tutorials. This section is the place to start for new users of the program and should also be examined by users of previous versions of Spartan. Section III (Features and Functions, Chapters 12 to 22) describes in detail the functions available from the menus and dialogs incorporated into the graphical user interface for Spartan. The focus is on graphical input and manipulation of structure, input of other required information and text, spectral and graphical output resulting from molecular mechanics and quantum chemical calculations, and on use of databases of previously-calculated structures, energies, properties and spectra accessible from Spartan. This section is intended as a general reference to Spartan’10. What this guide does not do is document the performance and cost (in computation time) of the different molecular mechanics and quantum chemical models available in Spartan’10, or recommend specific models or combinations of models for use on chemical problems. Nor does it show the utility of graphical models in presenting and interpreting the results of the calculations. These topics, among several others, are touched on in Appendix A (also available under Scope of this Guide i Topics from the Activities menu). They are also covered in depth in A Guide to Molecular Mechanics and Quantum Chemical Calculations included as a PDF under the Help menu and available from Wavefunction as a hardbound volume. The guide also provides a collection of illustrative examples. Additional appendices provide an overview of the program’s overall architecture as well as its present capabilities and limitations (B), a directory of functions under its menus (C), a listing of commonly- used options (D), a listing of units (E), the proper citation for the program (F), instructions for installing the Cambridge Structural Database (G), directions for making databases from Spartan calculations (H), examples of pharmacophore input (I), input of experimental infrared, UV/visible and NMR spectra (J), directions for installing a network HASP (K) and a listing of NMR chemical shift standards (L). Additional materials relating to several of these appendices may be found as PDFs under the Help menu. An up-to-date version of this Tutorial and User’s Guide is available on Wavefunction’s website (directly accessible from the Help menu). ii Scope of this Guide Table of Contents Section I INTRODUCTION ............................................. 1 Chapter 1 Spartan’10 ........................................................... 9 Section II GETTING STARTED ....................................... 17 Chapter 2 Operating Spartan ............................................. 19 Opening and Exiting Spartan .............................. 19 Menus .................................................................. 19 Keystroke Equivalents ......................................... 21 Icons ..................................................................... 21 Tabs ...................................................................... 22 Mouse and Keyboard Operations ........................ 23 Selection ............................................................ 23 Manipulation ..................................................... 24 Selecting Molecules, etc ...................................... 25 Dialogs ................................................................. 26 Database Access ................................................... 27 Stereo Displays .................................................... 27 Changing Colors and Setting Preferences ........... 27 Monitoring and Terminating Jobs ........................ 27 Chapter 3 Basic Operations ................................................ 29 Chapter 4 Organic Molecules ............................................. 47 Acrylonitrile ......................................................... 49 Cyclohexanone..................................................... 57 Camphor .............................................................. 60 Ethinamate ........................................................... 63 3-Cyano-4-methylcyclohexenyl Radical ............. 65 Androsterone ........................................................ 68 Chapter 5 Groups of Organic Molecules ........................... 71 Dienophiles in Diels-Alder Cycloadditions ......... 73 Addition vs. Substitution ..................................... 79 Allyl Vinyl Ether .................................................. 81 Internal Rotation in Dimethylperoxide ................ 84 Table of Contents iii Hydration of Carbonyl Compounds ..................... 88 Acidities of Carboxylic Acids .............................. 92 Positional Selectivities of Substituted Naphthalenes ........................................................ 95 Tautomers of Nucleotide Bases ........................... 98 Chapter 6 Spectra of Organic Molecules ........................... 101 Infrared Spectrum of Methyl Formate ................. 103 Searching Spartan’s Infrared Spectral Database .. 106 Proton NMR Spectrum of 2-Norbornene............. 110 13C NMR Spectrum of Caulophylline .................. 115 13C NMR Spectrum of cis-1,2-Dimethylcyclohexane .............................. 117 Stereochemical Assignments from 13C Spectra.... 119 13C Chemical Shifts Depend on Conformation .... 121 Chapter 7 Organic Reactions .............................................. 123 Ene Reaction of 1-Pentene ................................... 125 SN2 Reaction of Bromide and Methyl Chloride ... 129 Carbene Additions to Alkenes.............................. 133 Stereospecific Diels-Alder Reactions .................. 137 Thermodynamic vs. Kinetic Control ................... 140 Activation Energies of Diels-Alder Reactions ..... 143 Chapter 8 Medicinal Chemistry ......................................... 147 Anticipating Blood-Brain Transport .................... 149 Terfenadine. A Potassium Channel Blocker? ....... 152 Morphine. Structure vs. Pharmacophore ............. 155 Chapter 9 Polypeptides to Proteins .................................... 163 Polyglycine .......................................................... 165 Gleevec. Protein-Bound vs. Free Conformer....... 169 Gleevec. Making a Pharmacophore from PDB ... 173 Chapter 10 Inorganic and Organometallic Molecules........ 177 Sulfur Tetrafluoride .............................................. 179 Reactivity of Silicon-Carbon Double Bonds ....... 182 Benzene Chromium Tricarbonyl .......................... 185 Ziegler-Natta Polymerization of Ethylene ........... 187 iv Table of Contents Chapter 11 “Dry Labs”: Using the Spartan Spectra and Properties Database ........................................... 189 Isomeric C5H8 Dienes .......................................... 191 Using Infrared Spectroscopy to Identify an Unknown Ethyl Benzoate Derivative .................. 193 Infrared Spectra of Short-Lived Molecules ......... 196 Using 13C NMR to Distinguish Structural Isomers ................................................................. 198 Using 13C NMR Spectra to Distinguish Stereoisomers ....................................................... 201 Finding Stable Enols ............................................ 203 Electrophilic Reactivity of Polycyclic Aromatics. 205 Section III. FEATURES AND FUNCTIONS ...................... 207 Chapter 12 The File Menu .................................................... 209 New ...................................................................... 209 Open ..................................................................... 209 Close ...................................................................
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