ChemBioDraw 14.0 User Guide ChemBioDraw 14.0 Table of Contents Recent Additions vi Chapter 1: Introduction 1 About this Guide 1 Chapter 2: Getting Started 4 About ChemBioDraw Tutorials 4 ChemBioDraw User Interface 4 Toolbars 5 Documents 6 Chapter 3: Page Layout 10 The Drawing Area 10 The Document Type 10 Printing 12 Saving Page Setup Settings 13 35mm Slide Boundary Guides 13 Viewing Drawings 14 Tables 16 Chapter 4: Preferences and Settings 20 Setting Preferences 20 Customizing Toolbars 23 Document and Object Settings 23 Customizing Hotkeys 33 Working with Color 35 Document Settings 38 Chapter 5: Shortcuts and Hotkeys 44 Atom Keys 44 Bond Hotkeys 45 Function Hotkeys 46 © Copyright 1998-2014 CambridgeSoft Corporation, a subsidiary of PerkinElmer, Inc. All rights reserved. i ChemBioDraw 14.0 Shortcuts 47 Nicknames 50 Chapter 6: Basic Drawings 52 Bonds 52 Atoms 57 Captions 58 Drawing Rings 67 Chains 69 Objects 71 Clean Up Structure 88 Checking Structures 89 Chemical Warnings 89 Chapter 7: BioDraw (Ultra feature only) 92 BioDraw Templates 92 Customizable Objects 95 Chapter 8: Drawing Biopolymers 101 Biopolymer Editor 102 Protecting Groups 103 Pasting Sequences 104 Expanding Sequences 106 Contracting Labels 106 Modifying Sequence Residues 107 Merging Sidechains with Residue 107 Hybrid Biopolymers 110 IUPAC Codes 111 Disulfide Bridges 115 Lactam Bridges 116 Chapter 9: Advanced Drawing Techniques 118 Coloring Objects 118 © Copyright 1998-2014 CambridgeSoft Corporation, a subsidiary of PerkinElmer, Inc. All rights reserved. ii ChemBioDraw 14.0 Labels 119 Attachment Points 122 Atom Numbering 124 Structure Perspective 125 Mass Fragmentation 126 Drawing Reactions 127 Stoichiometry Grid 133 Templates 136 Defining Nicknames 138 ChemScript 141 Chapter 10: Struct=Name (Ultra Feature) 143 Struct>Name 143 Name>Struct 147 Chapter 11: Chemistry Features 149 Structure Analysis 149 ChemBioFinder hotlink 150 Stereochemistry 151 Chemical Annotations 154 Chemical Properties 158 3D Viewing 165 TLC 168 ChemNMR (Ultra Feature) 173 Chapter 12: ChemDraw/Excel and CombiChem 180 Setting Up ChemDraw/Excel 180 Importing tables 180 Importing hit lists 181 Exporting tables 181 Synchronizing Tables 182 Adding structures 183 © Copyright 1998-2014 CambridgeSoft Corporation, a subsidiary of PerkinElmer, Inc. All rights reserved. iii ChemBioDraw 14.0 Searching 184 R-Group analysis 185 Working with Structures 186 ChemDraw/Excel Functions 188 Chemical Properties 202 General Preferences 210 CombiChem 212 Chapter 13: ChemScript 220 Why use ChemScript? 220 How ChemScript works 221 Getting Started 221 Editing Scripts 222 Introducing the ChemScript API 223 Tutorials 224 Useful References 227 Chapter 14: Query Structures 228 Search Limitations 228 Generic Labels 228 Atom Properties 231 Bond Properties 239 Element Lists 242 Polymers 243 Link Nodes 247 Alternative Groups 248 Anonymous Alternative Groups 254 Expand Generic Structures 255 Atom-to-Atom Mapping 257 Stereochemical Symbols 260 3D Properties 261 © Copyright 1998-2014 CambridgeSoft Corporation, a subsidiary of PerkinElmer, Inc. All rights reserved. iv ChemBioDraw 14.0 Export Compatibility 262 Chapter 15: Sharing Information 267 The Clipboard 267 Transferring Objects 270 Embedding Objects 271 Exporting 271 Importing 272 Transferring Across Platforms 276 Chapter 16: Chemical Interpretation 277 Database Conventions 277 Chapter 17: Property Calculations 290 Chapter 18: ChemBioDraw Web Resources 293 Registering Online 293 User’s Guide 293 Technical Support 293 Querying SciFinder® with ChemBioDraw (Ultra Feature) 295 Chapter 19: Tutorials 298 Tutorial 1: Drawing a Structure 298 Tutorial 2: Drawing rings 299 Tutorial 3: Fischer projections 301 Tutorial 4: Perspective Drawings 304 Tutorial 5: Newman projections 308 Tutorial 6: Stereochemistry 311 Tutorial 7: Templates 314 © Copyright 1998-2014 CambridgeSoft Corporation, a subsidiary of PerkinElmer, Inc. All rights reserved. v ChemBioDraw 14.0 Recent Additions Windows 8.1, Microsoft Office 2013, and Mac OS X 10.9.x. ChemDraw strives to be a vital and preferred tool for illustrating chemical and biological concepts. Compatibility with the latest operating systems and tools is an essential part of that. Having the ChemDraw Active-X control functional with the latest browsers on both Windows and Mac platforms is part of this process, as well. ChemDraw to SciFinder Interface. Send ChemDraw structure and reaction queries directly to SciFinder to find useful information relevant to your com- pound/reaction. For more information, see "Querying SciFinder® with ChemBioDraw (Ultra Feature)" on page 295. Biopolymer Builder Enhancements. Single and multi letter amino acids - Lets you create single letter amino acids and nucleotides either by entering the corresponding IUPAC code, or by using the Biopolymer toolbar. The Biopolymer Editor lets you create three letter, or non-standard amino acids, by entering the residue name. Toggle Amino Acid Style AA1<->AA3 command - Lets you change the amino acid representation from single to multi-letter, and vice versa. For more information, see "Drawing Biopolymers" on page 101. L- and D- amino acids - Lets you create standard L- or D-amino acids by entering the relevant IUPAC code. Toggle L- and D-amino acids -The ‘Toggle Amino Acid Stereo L<->D’ command lets you change the ste- reochemistry of amino acids from L to D and vice versa. Protecting groups - Lets you add protecting groups such as Trt and Fmoc to amino acids containing additional NH 2 or OH groups (Arg, Aad). You can also expand and contract the protected residues. For more information, see "Pro- tecting Groups" on page 103. © Copyright 1998-2014 CambridgeSoft Corporation, a subsidiary of PerkinElmer, Inc. All rights vi reserved. ChemBioDraw 14.0 Cyclic and branched peptides - Lets you create cyclic peptides by bonding together the terminal residues in a pep- tide sequence. A looped bond indicates that the peptide is cyclic. You can create branched peptides using the sequence builder and bond tools. For more information, see "Cyclic, Crosslinked, and Branched Peptides" on page 113. Lactam bridges - Lets you form lactam bridges between residues with available amino and carboxylic acid leaving groups, such as Lys-Asp and Lys-Glu. For more information, see "Lactam Bridges " on page 116. Merging sequences - Lets you merge multiple sequences into one sequence by bonding together their terminal residues. Hybrid biopolymers - Lets you create hybrid (also called 'chimeric') biopolymers containing peptide, nucleotide, and linker residues, using the Biopolymer toolbar. For more information, see "Hybrid Biopolymers" on page 110. Pasting sequences - Lets you paste sequences in the FASTA format. You can also copy a text string describing a biopolymer as a series of single or multi letter residues, with valid separators (space, tab, dash), and paste it as a sequence. The text string can be generated within or outside of ChemBioDraw. See "Pasting Sequences" on page 104. Displaying expanded residues - Expanded residues can appear in either linear mode or zigzag mode. Expanding and contracting labels - Lets you expand the entire sequence, or any part of it. The sequence is auto- matically cleaned following expansion. When you contract a sequence, the Clean Up Biopolymer command cleans and re-arranges the sequence, so that the residues are aligned and wrapped. Numbering residues - Lets you display residue numbers above any residue. For more information, see "Numbering Residues" on page 110. Hide/Show termini and bonds - Lets you hide bonds and termini without affecting the underlying chemistry. Nickname Enhancements. In ChemBioDraw 14.0, many new residues, for example, non-standard amino acids, non-standard nucleotides, linkers have been added to the nickname library. Defining nicknames is much easier and more flexible now.For more inform- ation on nicknames, see "Defining Nicknames" on page 138. Struct>Name Enhancements. Struct>Name in ChemBioDraw 14.0 is enhanced to support many homopolymers, copolymers, and alternating poly- mers, and stoichiometry specified as bracket properties, including fractional stoichiometry. For more information, see "Struct>Name " on page 143. Electron Pushing. ChemBioDraw 14.0 introduces the Electron Pushing tool for illustrating electron transfer. For more information, see "Electron and Radical Pushing" on page 132. © Copyright 1998-2014 CambridgeSoft Corporation, a subsidiary of PerkinElmer, Inc. All rights reserved. vii ChemBioDraw 14.0 Gel Electrophoresis Tool. Gel electrophoresis separates molecules using an electric field applied to a gel matrix. The gel electrophoresis tool in ChemBioDraw 14.0 works much like the TLC tool and lets you easily draw and mark bands based on weight or dis- tance. For more information, see "TLC" on page 168. TLC Plate Enhancements. Lets you copy and drag spots between lanes. For more information, see "TLC" on page 168. Polymer Bead Enhancements. Lets you re-size polymer beads. For more information on polymer beads and other attachment points, see "Attach- ment Points" on page 122. New Toolbars. ChemBioDraw 14.0 introduces several new toolbars, including, Structure, Curves, Windows, and Biopolymer tool- bars. You access these toolbars from the View menu. Color by Element. Lets you color atom labels using colors associated with their atomic symbols, as shown in the example below. For more information, see "Color by Element" on page 36. New Property Predictions. Incorporates new calculations from Molecular Networks for predicting pKa, LogS