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Chem3D 17.0 User Guide Chem3D 17.0 Table of Contents Recent Additions viii Chapter 1: About Chem3D 1 Additional computational engines 1 Serial numbers and technical support 3 About Chem3D Tutorials 3 Chapter 2: Chem3D Basics 5 Getting around 5 User interface preferences 9 Background settings 10 Sample files 10 Saving to Dropbox 10 Chapter 3: Basic Model Building 12 Default settings 12 Selecting a display mode 12 Using bond tools 13 Using the ChemDraw panel 15 Using other 2D drawing packages 15 Building from text 16 Adding fragments 18 Selecting atoms and bonds 18 Atom charges 21 Object position 23 Substructures 24 Refining models 27 Copying and printing 29 Finding structures online 32 Chapter 4: Displaying Models 35 © Copyright 1998-2017 PerkinElmer Informatics Inc., All rights reserved. ii Chem3D 17.0 Display modes 35 Atom and bond size 37 Displaying dot surfaces 38 Serial numbers 38 Displaying atoms 39 Atom symbols 40 Rotating models 41 Atom and bond properties 44 Showing hydrogen bonds 45 Hydrogens and lone pairs 46 Translating models 47 Scaling models 47 Aligning models 47 Applying color 49 Model Explorer 52 Measuring molecules 59 Comparing models by overlay 62 Molecular surfaces 63 Using stereo pairs 72 Stereo enhancement 72 Setting view focus 73 Chapter 5: Building Advanced Models 74 Dummy bonds and dummy atoms 74 Substructures 75 Bonding by proximity 78 Setting measurements 78 Atom and building types 81 Stereochemistry 85 © Copyright 1998-2017 PerkinElmer Informatics Inc., All rights reserved. iii Chem3D 17.0 Building with Cartesian tables 87 Building models using ISIS/Draw 88 Lone electron pairs 88 Chapter 6: Computational Engines 89 Ab initio methods 89 Semi-empirical methods 89 Force field calculation methods 89 Compute properties 90 Calculating multiple properties 92 MM2 and MMFF94 92 Gaussian 105 CONFLEX 111 MOPAC 112 GAMESS 134 Chapter 7: Parameter Tables 141 The elements 143 Building types 143 Substructures table 146 References 147 Bond stretching parameters 147 Angle bending parameters 148 Conjugated Pisystem bonds 149 Pi Atoms 150 Electronegativity adjustments 150 MM2 constants 151 MM2 atom type parameters 153 Torsional parameters 154 Out-of-plane bending 156 © Copyright 1998-2017 PerkinElmer Informatics Inc., All rights reserved. iv Chem3D 17.0 van der Waals interactions 156 Chapter 8: Docking 158 Installing AutoDock 158 Installing AutoDock Tools 158 Configuring AutoDock 159 Working with the AutoDock Interface 159 Step 1: Preparing the receptor 160 Step 2: Preparing the ligand 161 Step 3: (Optional) Defining groups 162 Step 4: Preparing the cavity (prepare GPF) 162 Step 5: Selecting pose parameters (Prepare DPF) 164 Step 6: Docking 165 Step 7: Viewing Docking Results 165 References 166 Chapter 9: Computation Concepts 167 Computational chemistry overview 167 Computational methods overview 167 Uses of computational methods 168 Geometry optimization 168 Choosing the best method 170 Molecular mechanics theory in brief 174 The force-field 174 Molecular dynamics simulation 182 Chapter 10: ChemScript 184 Why use ChemScript? 184 How ChemScript works 185 Getting Started 185 Editing Scripts 186 © Copyright 1998-2017 PerkinElmer Informatics Inc., All rights reserved. v Chem3D 17.0 Introducing the ChemScript API 187 Tutorials 188 Useful References 191 Chapter 11: Chemical properties 194 Chem3D properties 194 ChemFinder properties 221 ChemDraw properties 222 ChemDraw/Excel properties 222 Chapter 12: Keyboard modifiers 224 Rotation 224 Selection 225 Chapter 13: 2D to 3D Conversion 227 Stereochemical relationships 227 Labels 228 Chapter 14: File Formats 230 Editing file format atom types 230 Native formats 230 File format examples 230 Export file formats 262 Chapter 15: References 272 MEP 272 MM2 references 273 MOPAC 275 Chapter 16: Online Resources 289 SciStore 289 PerkinElmer Informatics 289 Online documentation 289 Online registration 289 © Copyright 1998-2017 PerkinElmer Informatics Inc., All rights reserved. vi Chem3D 17.0 ChemOffice SDK 289 Troubleshooting 289 Chapter 17: Tutorials 291 Building models 291 Examining models 303 Using calculation engines 320 © Copyright 1998-2017 PerkinElmer Informatics Inc., All rights reserved. vii Chem3D 17.0 Recent Additions Chem3D introduces a variety of improvements not found in earlier versions. These are briefly described below. Microsoft Office 2013 and Windows 8.1.Chem3D is compatible with Microsoft Office 2013 and Windows 8.1 for both 32 and 64 bit machines. Depiction and animation of GAMESS IR Vibrations.After you compute an infrared spectrum, you can view and animate the IR vibration modes and the vectors that are applied. For more information, see "Viewing and animating GAMESS IR vibrations" on page 139. Molecular Orbital Calculations using GAMESS 2013 and MOPAC 2016.You can now calculate molecular orbit- als using either GAMESS 2013 or MOPAC 2016. By default, PM7 is the basis set in the latest version of MOPAC. Support for Gaussian 09.In addition to Gaussian 03, Chem3D also supports Gaussian 09. Gaussian can be pur- chased from PerkinElmer. Support for native 64-bit GAMESS 2013.GAMESS 2013 can be downloaded from using the link http://www.ms- g.ameslab.gov/gamess/index.html . Support for V3000 MolFile Format.For both import and export. 2D projections of 3D surfaces.The volume slicing tool lets you view a two-dimension cross section of almost any molecular surface. This becomes quite useful for viewing the electron density at any location in your model. You can slice through an orbital or an entire model in either the X-, Y-, or Z-planes and adjust the location of the slice as desired. For more information, see "Volume slicing" on page 71. Saving to Dropbox.Chem3D allows you to save to Dropbox for users with a Dropbox account. You can upload and download files between your remote Dropbox folder and your local machine. You can also use Dropbox to pass files between Chem3D and the Chem3D iPad app. The Dropbox plug-in can be downloaded from the Dropbox Web site. Docking.AutoDock helps you determine how one or more small molecules may be arranged to fit inside the cavity of a larger molecule. You choose the molecules, the cavity binding sites, and calculation parameters. AutoDock cal- culates and displays the conformers and positions of each small molecule that fit your requirements. For more information, see "Docking" on page 158. CONFLEX.CONFLEX is a conformational analysis package developed by the CONFLEX Corporation. Using CONFLEX, you can search for low energy conformers of a model and create a fragment for each one in its optimal © Copyright 1998-2017 PerkinElmer Informatics Inc., All rights reserved. viii Chem3D 17.0 state. For more information, see "CONFLEX" on page 111. Molecular Networks integration.Chem3D incorporates new features from Molecular Networks for determining pKa, LogS and LogP solubility properties. See "Chem3D properties" on page 194. Also see "About Molecular Networks" on page 2. © Copyright 1998-2017 PerkinElmer Informatics Inc., All rights reserved. ix Chem3D 17.0 About Chem3D Chem3D is part of the ChemOffice suite and lets you build, visualize, and analyze 3D models of chemical structures. Chem3D models can be imported into desktop publishing tools or displayed on the Web. Additional computational engines Chem3D supports several additional computational engines. These tools are briefly mentioned below. Their full descriptions are found in respective chapters of this guide. For availability and purchase information, contact PerkinElmer Informatics. About GAMESS GAMESS is a program for ab initio molecular quantum chemistry calculations. GAMESS lets you predict UV/VIS, IR and NMR spectra, calculate energies and a number of other molecular properties. About Gaussian Chem3D supports Gaussian 03 and Gaussian 09. Gaussian is a property prediction program used by chemists, chem- ical engineers, biochemists, physicists, and other scientists. Using the ab initio and semi-empirical quantum mech- anics, Gaussian predicts the energies, molecular structures, vibrational frequencies and chemical properties of molecules and reactions in a variety of chemical environments. You can apply Gaussian to both stable compounds and compounds that are difficult or impossible to observe experimentally such as short-lived intermediates and trans- ition structures. Gaussian supports ab initio methods, such as restricted and unrestricted Hartree Fock methods. You can use ab initio and semi-empirical methods for calculating electron density surface and molecular geometry optimization. Gaussian supports ground state semi-empirical methods such as CNDO/2, INDO, MINDO3, and MDO energies and gradients. Note: The term "semi-empirical" refers to methods that use the general process dictated by quantum mechanics, but simplify it to gain speed and later use experimental data to compensate for the simplification. Note: Gaussian 03 requires 32-bit version of Windows and Gaussian 09 requires either 32-bit version or 64-bit ver- sion of Windows. See "Gaussian" on page 105 for more information. About MOPAC MOPAC performs semi-empirical calculations on atoms and molecules to determine details of molecular structures and properties. For example, with MOPAC you can perform thermodynamic calculations, geometry optimizations, and force constant calculations.Chem3D supports MOPAC 2016. Functionalities of MOPAC are provided through a Chem3D interface. MOPAC2016 includes all the capabilities of MOPAC, and is available only as an optional plug-in. MOPAC 2016 provides support for advanced features,
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