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Users Guide
CS ChemDraw 8.0
for Windows and Macintosh
ChemDraw is a stand alone application within
ChemOfce, an integrated suite including
Chem3D for molecular modeling and analysis,
ChemFinder for searching and information integration,
ChemInfo for chemical and reference databases, and
E-Notebook for electronic journal and information.
ChemDraw
License Information
ChemOffice, ChemDraw, Chem3D, ChemFinder, and ChemInfo programs, all resources in the ChemOffice,
ChemDraw, Chem3D, ChemFinder, and ChemInfo application files, and this manual are Copyright 1986-2003
by CambridgeSoft Corporation (CS) with all rights reserved worldwide. MOPAC 2000 is Copyright 1993-2003
by Fujitsu Limited with all rights reserved. Information in this document is subject to change without notice and
does not represent a commitment on the part of CS. Both these materials and the right to use them are owned exclusively by CS. Use of these materials is licensed by CS under the terms of a software license agreement; they may be
used only as provided for in said agreement.
ChemOffice, ChemDraw, Chem3D, CS MOPAC, ChemFinder, and ChemInfo are not supplied with copy protection. Please do not duplicate any of the copyrighted materials except for your personal backups without written permission from CS. To do so would be in violation of federal and international law, and may result in criminal as well
as civil penalties. You may use ChemOffice, ChemDraw, Chem3D, CS MOPAC, ChemFinder and ChemInfo on
any computer owned by you; however, extra copies may not be made for that purpose. Consult the CS License
Agreement for further details.
Trademarks
ChemOffice, ChemDraw, Chem3D, ChemFinder, ChemInfo and ChemACX are registered trademarks of
CambridgeSoft Corporation (Cambridge Scientific Computing, Inc.).
The Merck Index is a registered trademark of Merck & Co., Inc. 2001 All rights reserved.
MOPAC 2000 and MOPAC are trademarks of Fujitsu Limited.
Microsoft Windows, Windows NT, Windows 95, and Microsoft Word are registered trademarks of Microsoft Corp.
Apple Events, Macintosh, Laserwriter, Imagewriter, QuickDraw and AppleScript are registered trademarks of Apple
Computer, Inc. Geneva, Monaco, and TrueType are trademarks of Apple Computer, Inc.
The ChemSelect Reaction Database is copyrighted by InfoChem GmbH 1997.
AspTear is copyrighted by Softwing.
Copyright 1986-2003 CambridgeSoft Corporation (Cambridge Scientific Computing, Inc.) All Rights Reserved.
Printed in the United States of America.
All other trademarks are the property of their respective holders.
CambridgeSoft End-User License Agreement for Software Products
Important: This CambridgeSoft License Agreement (Agreement) is a legal agreement between you, the end user
(either an individual or an entity), and CambridgeSoft Corporation (CS) regarding the use of CS Software
Products, which may include computer software, the associated media, any printed materials, and any online or
electronic documentation. By installing, copying, or otherwise using any CS Software Product, you signify that you
have read the CS License Agreement and agree to be bound by its terms. If you do not agree to the Agreements terms,
promptly return the package and all its contents to the place of purchase for a full refund.
5. Separation of Components. The Software is licensed as a single product. Its component parts may not be separated for use on more than one computer, except in the case of the ChemOffice WebServer. The ChemOffice
WebServer includes five (5) licenses for the ChemDraw Plugin and five (5) licenses for the Chem3D Plugin. The
Plugin software products may be installed on computers other than that one on which the ChemOffice WebServer
is installed. However, each copy of the Plugin is individually subject to the provisions of Paragraphs 1 through 4 of
this Agreement. Network based access to the ChemDraw Java applet may be substituted for each installation of the
ChemDraw Plugin, as long as the sum of the number of workstations using ChemOffice WebServer with either the
ChemDraw Java applet or the ChemDraw Plugin is five (5) or less.
6. Educational Use Only of Student Licenses. If you are a student enrolled at an educational institution, the CS
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CS Limited Warranty
Limited Warranty. CSs sole warranty with respect to the Software is that it shall be free of errors in program logic
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CSs Liability. In no event shall CS be liable for any indirect, special, or consequential damages, such as, but not
limited to, loss of anticipated profits or other economic loss in connection with or arising out of the use of the software by you or the services provided for in this agreement, even if CS has been advised of the possibility of such damages. CSs entire liability and your exclusive remedy shall be, at CSs discretion, either (A) return of any license fee,
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NO OTHER WARRANTIES. CS DISCLAIMS OTHER IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
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No Waiver. The failure of either party to assert a right hereunder or to insist upon compliance with any term or condition of this Agreement shall not constitute a waiver of that right or excuse a similar subsequent failure to perform
any such term or condition by the other party.
Governing Law. This Agreement shall be construed according to the laws of the Commonwealth of Massachusetts.
Export. You agree that the Software will not be shipped, transferred, or exported into any country or used in any manner prohibited by the United States Export Administration Act or any other export laws, restrictions, or regulations.
End-User License Agreement for CambridgeSoft Database Products
Important: This CambridgeSoft End-User License Agreement (EULA) is a legal agreement between you (either an
individual or a single entity) and CambridgeSoft Corporation for the CambridgeSoft supplied database product(s)
and may include associated media, printed materials, and online or electronic documentation. By using the database product(s) you agree that you have read, understood and will be bound by this license agreement.
Database Product License
1. Copyright Notice. The materials contained in CambridgeSoft Database Products, including but not limited to,
ChemACX, ChemIndex, and The Merck Index, are protected by copyright laws and international copyright treaties,
as well as other intellectual property laws and treaties. Copyright in the materials contained on the CD and internet
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artwork, photographs, computer software, audio and visual elements, is owned or controlled separately by
CambridgeSoft Corporation (CS).
CS is a distributor (and not a publisher) of information supplied by third parties. Accordingly, CS has no editorial
control over such information. Database Suppliers (Supplier) individually own all right, title, and interest, including copyright, in their databaseand retain all such rights in providing information to Customers.
The materials contained in The Merck Index are protected by copyright laws and international copyright treaties, as
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subscription products, including, but not limited to, the textual material, chemical structures representations, artwork, photographs, computer software, audio and visual elements, is owned or controlled separately by the Merck &
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2. Limitations on Use. Except as expressly provided by copyright law, copying, redistribution, or publication,
whether for commercial or non-commercial purposes, must be with the express permission of CS and/or Merck. In
any copying, redistribution, or publication of copyrighted material, any changes to or deletion of author attribution
or copyright notice, or any other proprietary notice of CS, Merck, or other Database producer are prohibited.
3. Grant of License, CD Databases. CambridgeSoft Software Products are licensed, not sold. CambridgeSoft grants
and you hereby accept a nonexclusive license to use one copy of the enclosed Software Product (Software) in accordance with the terms of this Agreement. This licensed copy of the Software may only be used on a single computer,
except as provided below. You may physically transfer the Software from one computer to another for your own use,
provided the Software is in use (or installed) on only one computer at a time. If the Software is permanently installed
on your computer (other than a network server), you may also use the Software on a portable or home computer,
provided that you use the software on only one computer at a time. You may not (a) electronically transfer the
Software from one computer to another, (b) distribute copies of the Software to others, or (c) modify or translate the
Software without the prior written consent of CambridgeSoft, (d) place the software on a server so that it is accessi-
ble via a public network such as the Internet, (e) sublicense, rent, lease or lend any portion of the Software or
Documentation, or (f ) modify or adapt the Software or merge it into another program. The Software may be placed
on a file or disk server connected to a network, provided that a license has been purchased for every computer with
access to that server. You may make only those copies of the Software which are necessary to install and use it as permitted by this agreement, or are for purposes of backup and archival records; all copies shall bear CambridgeSofts
copyright and proprietary notices. You may not make copies of any accompanying written materials.
4. Assignment Restrictions for CD databases. You may not rent, lease, or otherwise sublet the Software or any part
thereof. You may transfer on a permanent basis the rights granted under this license provided you transfer this
Agreement and all copies of the Software, including prior versions, and all accompanying materials. The recipient
must agree to the terms of this Agreement in full and register this transfer in writing with CambridgeSoft.
5. Revocation of Subscription Access. Any use which is commercial and/or non-personal is strictly prohibited, and
may subject the Subscriber making such uses to revocation of access to this Paid Subscription Service, as well as any
other applicable civil or criminal penalties. Similarly, sharing a Subscriber password with a non-Subscriber or otherwise making this Paid Subscription Service available to third parties other than the Authorized User as defined above
is strictly prohibited, and may subject the Subscriber participating in such activities to revocation of access to the Paid
Subscription Services; and, the Subscriber and any third party, to any other applicable civil or criminal penalties
under copyright or other laws. In the case of an authorized site license, a Subscriber shall cause any employee, agent
or other third party which the Subscriber allows to use the Paid Subscription Service materials to abide by all of the
terms and conditions of this Agreement. In all other cases, only the Subscriber is permitted to access the Paid
Subscription Service materials. Should CambridgeSoft become aware of any use that might cause revocation of the
license, they shall notify the Subscriber. The Subscriber shall have 90 days from date of notice to correct such violation before any action will be taken.
6. Trademark Notice. THE MERCK INDEX is a trademark of Merck & Company Incorporated, Whitehouse
Station, New Jersey, USA and is registered in the United States Patent and Trademark Office. CambridgeSoft and
ChemACX are trademarks of CambridgeSoft Corporation, Cambridge, Massachusetts, USA and are registered in the
United States Patent and Trademark Office, the European Union (CTM) and Japan.
Any use of the marks in connection with the sale, offering for sale, distribution or advertising of any goods and services, including any other website, or in connection with labels, signs, prints, packages, wrappers, receptacles or
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7. Modification of Databases, Websites, or Subscription Services. CS reserves the right to change, modify, suspend or discontinue any or all parts of any Paid Subscription Services and databases at any time.
8. Representations and Warranties. The User shall indemnify, defend and hold CS, Merck, and/or other Supplier
harmless from any damages, expenses and costs (including reasonable attorneys fees) arising out of any breach or
alleged breach of these Terms and Conditions, representations and/or warranties herein, by the User or any third
party to whom User shares her/his password or otherwise makes available this Subscription Service. The User shall
cooperate in the defense of any claim brought against CambridgeSoft, Merck, and/or other Database Suppliers.
In no event shall CS, Merck, and/or other Supplier be liable for any indirect, special, or consequential damages, such
as, but not limited to, loss of anticipated profits or other economic loss in connection with or arising out of the use
of the software by you or the services provided for in this agreement, even if CS, Merck, and/or other Supplier has
been advised of the possibility of such damages. CS and/or Mercks entire liability and your exclusive remedy shall
be, at CSs discretion a return of any pro-rata portion of the subscription fee.
The failure of either party to assert a right hereunder or to insist upon compliance with any term or condition of this
Agreement shall not constitute a waiver of that right or excuse a similar subsequent failure to perform any such term
or condition by the other party.
This Agreement shall be construed according to the laws of the Commonwealth of Massachusetts, United States of
America.
ChemDraw
Chem3D
ChemFinder
Desktop Applications
E-Notebook Desktop
ChemDraw/Excel
ChemFinder/Office
CombiChem/Excel
ChemSAR/Excel
MOPAC, MM2
CS Gaussian, GAMESS Interface
Purchase/Excel
ChemOffice WebServer
Oracle Cartridge
Enterprise Solutions
E-Notebook Enterprise
Document Manager
Registration System
Formulations & Mixtures
Inventory Manager
Discovery LIMS
BioAssay HTS
BioSAR Browser
ChemDraw/Excel
ChemACX
ChemSCX
ChemMSDX
ChemINDEX
ChemRXN
NCI & AIDS
Tips
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Contents
Section I: ChemDraw
.......................1
Whats New in ChemDraw 8 . . . . . . . . . . . . . . . 1
For Users of ChemDraw 7 . . . . . . . . . . . . . . . . . 2
For Users of ChemDraw 5 or 6 . . . . . . . . . . . . . . 2
3
3
3
3
3
4
4
4
4
4
..............5
The ChemDraw Graphical User Interface . . . 5
The Main Tools Palette . . . . . . . . . . . . . . . . . . . . 6
Setting the Default Tool. . . . . . . . . . . . . . . . . . . . 8
Tearing Off Palettes . . . . . . . . . . . . . . . . . . . . . . . 8
Optional Toolbars. . . . . . . . . . . . . . . . . . . . . . . . . 8
Showing and Hiding Toolbars . . . . . . . . . . . . . . 9
Docking and Undocking Toolbars . . . . . . . . . . . 9
The Status Bar or Message Area (Windows). . . 9
The Analysis Window . . . . . . . . . . . . . . . . . . . . . 9
The Chemical Properties Window . . . . . . . . . . 10
The Info Window . . . . . . . . . . . . . . . . . . . . . . . . 10
Periodic Table . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Character Map . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Customizing ChemDraw. . . . . . . . . . . . . . . . . . 12
Setting Preferences. . . . . . . . . . . . . . . . . . . . . . . 12
Document and Object Settings . . . . . . . . . . . . . 12
Default Style Sheet or Stationery Pad . . . . 12
Saving Customized Settings as Style
Sheets or Stationery Pads . . . . . . . . . . . . . 13
Applying Document Settings From
Other Documents . . . . . . . . . . . . . . . . . . . . 13
Applying Object Settings from
Other Documents . . . . . . . . . . . . . . . . . . . . 14
Using Documents. . . . . . . . . . . . . . . . . . . . . . . . 14
Setting the Default Document Location. . . . . . 14
ChemDraw 8
Chapter 2: Tutorials . . . . . . . . . . . . . . . . . . . . . . .
21
Contents
Administrator
ii
Contents
49
CambridgeSoft
81
82
82
82
83
83
83
83
88
88
89
89
Framing Objects . . . . . . . . . . . . . . . . . . . . . . . . .
The Arc Tools Palette . . . . . . . . . . . . . . . . . . . .
Drawing Arcs . . . . . . . . . . . . . . . . . . . . . . . . . . .
Editing Arcs . . . . . . . . . . . . . . . . . . . . . . . . . . . .
89
89
89
89
90
90
91
91
92
92
92
92
92
ChemDraw 8
97
109
Contents
iii
Administrator
Chapter 9:
Drawing Query Structures . . . . . . . . . . . . . . . 137
Atom Properties . . . . . . . . . . . . . . . . . . . . . . . . 137
Viewing Atom Property Values . . . . . . . . . . . 138
Removing Atom Properties . . . . . . . . . . . . . . . 138
Atom Property Options. . . . . . . . . . . . . . . . . . 138
Substituents . . . . . . . . . . . . . . . . . . . . . . . . . . . . 139
Implicit Hydrogens . . . . . . . . . . . . . . . . . . . . . 139
Ring Bond Count . . . . . . . . . . . . . . . . . . . . . . . 140
Unsaturation . . . . . . . . . . . . . . . . . . . . . . . . . . . 140
Reaction Change . . . . . . . . . . . . . . . . . . . . . . . 141
Reaction Stereo. . . . . . . . . . . . . . . . . . . . . . . . . 141
Translation . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141
Isotopic Abundance . . . . . . . . . . . . . . . . . . . . . 141
Abnormal Valence . . . . . . . . . . . . . . . . . . . . . . 142
iv
Contents
127
CambridgeSoft
151
151
152
152
152
153
154
154
154
155
156
156
157
166
167
167
167
167
167
167
168
Arranging Objects . . . . . . . . . . . . . . . . . . . . . .
Using Rulers . . . . . . . . . . . . . . . . . . . . . . . . . . .
Showing Rulers . . . . . . . . . . . . . . . . . . . . . . . .
Hiding Rulers . . . . . . . . . . . . . . . . . . . . . . . . . .
Using the Crosshair . . . . . . . . . . . . . . . . . . . . .
168
168
168
169
169
ChemDraw 8
177
Contents
Administrator
.ChemDraw/Excel . . . . . . . . . . . . . . . . . . . . . . . . . 201
Starting ChemDraw/Excel . . . . . . . . . . . . . . . 201
Setting Excel Security . . . . . . . . . . . . . . . . . . . 201
Importing Tables. . . . . . . . . . . . . . . . . . . . . . . . 201
Converting and Updating a Worksheet . . . 202
Importing Hit Lists . . . . . . . . . . . . . . . . . . . . . . 202
Importing a Hitlist . . . . . . . . . . . . . . . . . . . . . . 202
Error Messages . . . . . . . . . . . . . . . . . . . . . . . . . 203
Exporting Tables. . . . . . . . . . . . . . . . . . . . . . . . 203
Adding Molecules. . . . . . . . . . . . . . . . . . . . . . . 204
Adding Molecules with ChemDraw . . . . . . . . 204
Adding Structure Files . . . . . . . . . . . . . . . . . . . 204
Adding SMILES Strings . . . . . . . . . . . . . . . . . 204
Adding Molecules by Name . . . . . . . . . . . . . . 205
Saving Molecules . . . . . . . . . . . . . . . . . . . . . . . 205
Searching . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 205
Filter Tables . . . . . . . . . . . . . . . . . . . . . . . . . . . 205
Similarity Searches . . . . . . . . . . . . . . . . . . . . . 206
CAMEO
ChemDraw/Excel . . . . . . . . . . . . . . . . . . . . . . . .199
CAMEO/Excel . . . . . . . . . . . . . . . . . . . . . . . . . . .199
vi
Contents
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 213
199
Installation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 213
Minimum System Requirements . . . . . . . . . . 214
Operating System Options . . . . . . . . . . . . 214
Software Requirements . . . . . . . . . . . . . . . 214
Configuring and Starting CAMEO/Excel . . 214
From ChemDraw . . . . . . . . . . . . . . . . . . . . . 214
From Excel . . . . . . . . . . . . . . . . . . . . . . . . . . 214
Submitting a Reaction. . . . . . . . . . . . . . . . . . . 215
Reaction Module . . . . . . . . . . . . . . . . . . . . . . . 215
Reaction Parameters. . . . . . . . . . . . . . . . . . . . . 215
Reaction Condition . . . . . . . . . . . . . . . . . . . 215
Temperature Range . . . . . . . . . . . . . . . . . . 216
Stoichiometry . . . . . . . . . . . . . . . . . . . . . . . . 216
Reagent . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 216
CambridgeSoft
Appendix B:
How ChemProp/Draw Works . . . . . . . . . . . A13
Creating a Script. . . . . . . . . . . . . . . . . . . . . . . .
Reaction Parameters Tab . . . . . . . . . . . . . . . . .
Display Option Parameters Tab . . . . . . . . . . .
Cdx Input From File . . . . . . . . . . . . . . . . . .
Result Display Layout . . . . . . . . . . . . . . . .
Reporting Options for Excel . . . . . . . . . . .
Save and Append . . . . . . . . . . . . . . . . . . . . . . .
218
218
219
219
219
219
220
Editing a Script . . . . . . . . . . . . . . . . . . . . . . . . .
Save Reaction . . . . . . . . . . . . . . . . . . . . . . . . . .
Next . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Exit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
220
221
221
221
Appendices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A1
Appendix A: The Chemistry of ChemDraw
A3
Database Conventions . . . . . . . . . . . . . . . . . . .A3
Chemical Conventions . . . . . . . . . . . . . . . . . . .A4
Atom Labels . . . . . . . . . . . . . . . . . . . . . . . . . . . .A4
Chemically Significant Text . . . . . . . . . . . . . . .A5
Charges . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .A6
Isotopes and Elements . . . . . . . . . . . . . . . . . . . .A7
Radicals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .A7
H-Dot/H-Dash . . . . . . . . . . . . . . . . . . . . . . . . . .A7
Complexes . . . . . . . . . . . . . . . . . . . . . . . . . . . . .A7
Multi-center Attachments . . . . . . . . . . . . . . . . .A8
Stereochemistry . . . . . . . . . . . . . . . . . . . . . . . . .A8
Stereochemical Indicators . . . . . . . . . . . . . .A9
Stereochemical Flags . . . . . . . . . . . . . . . . . . . . .A9
Polymer Representations . . . . . . . . . . . . . . . . .A10
References . . . . . . . . . . . . . . . . . . . . . . . . .A10
Query Properties. . . . . . . . . . . . . . . . . . . . . . . .A10
ChemDraw 8
LogP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Henrys Law . . . . . . . . . . . . . . . . . . . . . . . . . . .
Molar Refractivity . . . . . . . . . . . . . . . . . . . . . .
ClogP and CMR . . . . . . . . . . . . . . . . . . . . . . . .
A13
A13
A14
A14
Appendix C:
How ChemNMR Pro Works
. . . . . . . . . . . . A15
ChemNMR Limitations . . . . . . . . . . . . . . . . . . A15
Appendix D: Automation
. . . . . . . . . . . . . . . . A17
Macintosh . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A17
Windows . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A17
. . . . . . . . . A19
ChemDraw Style Sheets or
Stationery Pads . . . . . . . . . . . . . . . . . . . . . . . A20
. . . A31
Connection Table File Format . . . . . . . . . . . A31
. . . . . . . . . A35
Serial Numbers . . . . . . . . . . . . . . . . . . . . . . . . A35
Macintosh . . . . . . . . . . . . . . . . . . . . . . . . . . . . A35
Windows . . . . . . . . . . . . . . . . . . . . . . . . . . . . . A35
Troubleshooting . . . . . . . . . . . . . . . . . . . . . . .
Launching . . . . . . . . . . . . . . . . . . . . . . . . . . . .
Performance . . . . . . . . . . . . . . . . . . . . . . . . . . .
System Crashes . . . . . . . . . . . . . . . . . . . . . . . .
A36
A36
A36
A36
A39
A42
A43
A43
A44
A45
A46
A47
Index
Contents
vii
Administrator
viii
Contents
CambridgeSoft
Section I: ChemDraw
This section describes the ChemDraw application.
Section 2 describes ChemDraw addins.
ChemDraw is a tool to enable professional
scientists, science students, and scientific authors to
communicate chemical structures. It is designed to
work according to conventions we found most
intuitive for such users. Our goal has been to make
ChemDraw as easy to use as possible while
providing superior drawing quality.
Whats New in
ChemDraw 8
ChemDraw 8 is enhanced by the following features:
Completely rewritten Struct=Name
Generate systematic names for chemical
structures, including comprehensive support for
the Cahn-Ingold-Prelog (CIP) rules for absolute
stereochemistry (R, S, E, Z, etc.). See Adding
Chemical Names on page 72.
Floating periodic table and character map
Keep information about all elements at your
fingertips. It's now even easier to create labeled
atoms and to add special characters from any
font with ease. See Periodic Tableand
Character Map on page 11.
Improved Carbon-13 NMR predictions
Shift values are, on average, more than twice as
accurate as before. See NMR Shift
InformationChemNMR on page 135.
ChemDraw 8
Section I: ChemDraw
Whats New in ChemDraw 8
ChemDraw
Overview
ChemDraw 5 ChemDraw 8
or 6
Analyze
Structure
Caption Text
Settings
File menu
Pro
Chemical
Properties
Ultra
CLogP menu
(6.0.2 or later)
View menu,
Show Chemical
Properties
window
File menu
Color menu or
Document
Settings dialog
box
CLogP
Color Palette
Object menu,
Settings,
Captions tab
Section I: ChemDraw
Feature
ChemDraw 5 ChemDraw 8
or 6
Document
Setup
File menu
File Menu,
Document
Settings, Layout
and Footer tabs
Drawing
Settings
File menu
File menu,
Document
Settings,
Drawing tab
Label Text
Settings
File Menu
File menu,
Document
Settings, Atom
Labels tab
m/e values
Status bar
View menu,
Show Analysis
window
Positioning
and size
information
Status bar
View menu,
Show Info
window, or in
drawing area
Fixed lengths
and angles
Tools menu
Object menu
Format
Text menu
File menu,
Document
Settings,
Captions and
Atom Labels tab
Edit menu
CambridgeSoft
Whats New in ChemDraw 8
Feature
ChemDraw 5 ChemDraw 8
or 6
Estimate or
Scripts menu
Structure menu
Tools menu
items
Tools menu
View menu
Conventions
The following notations are used throughout this
users guide:
ChemDraw 8
ChemDraw
NMR
estimates
Additional Information
Additional sources of ChemDraw information are:
The Quick Reference Card.
The Help system
CambridgeSoft Web Pages.
http://www.cambridgesoft.com/support
Help System
ChemDraw provides the following types of Help:
HelpAn HTML reference guide.
Section I: ChemDraw
About This Users Guide
Administrator
Access
Technical
Support
http://www.cambridgesoft.com/
support/
ChemDraw
Plugin
http://www.cambridgesoft.com/
support/documentation/chemdra
wplugin/
Microsoft Windows
Requirements
Windows 98, Me, NT4 (SP-6 or higher), 2000,
or XP
MicrosoftOffice add-ins require Office 2000
or XP.
Plugins/ActiveX controls support Netscape 6.2
or greater, Mozilla 1.x, and MicrosoftInternet
Explorer 5.x and 6.x.
Macintosh Requirements
Software
http://sdk.cambridgesoft.com/
Developers kit
ActiveX
control
http://sdk.cambridgesoft.com/
http://chemstore.cambridgesoft.
Purchasing
CambridgeSoft com/
products and
chemicals
Section I: ChemDraw
CambridgeSoft
Installation and System Requirements
The ChemDraw
Graphical User Interface
Although the Macintosh and Windows versions of
the ChemDraw graphical user interface (GUI) differ
slightly, the essential GUI consists of the same
elements. The Windows version of ChemDraw is
shown below.
Magnification control
Title bar
Menu bar
Object toolbar
Minimize button
Maximize button
Close button
Text style
toolbar
General
toolbar
Scroll bars
Main tool
palette
Status bar
ChemDraw 8
Resize
ChemDraw
Overview
Administrator
Magnification control
Object toolbar
Menu bar
General
toolbar
Title bar
Scroll bar
Main tool
palette
Resize
Tool
Use to
Structure
Rotate a selected object in three
Perspective dimensions.
Ultra
Mass Fragmentation
tool
Tool
Use to
Bond
Selection
Eraser
Multiple
Bonds
CambridgeSoft
The Main Tools Palette
Use to
Tool
Use to
Text
Query
Tools
Pen
Arrow
Templates
Rings
Table
TLC Plate
Orbital
Drawing
Elements
Chemical
Symbols
Arc
Acyclic
Chain
ChemDraw 8
ChemDraw
Tool
Lasso
Administrator
Structure Perspective
Solid Bond
Marquee
Mass Fragment
Eraser
Multiple Bonds
Text
Dashed Bond
Pen
Hashed Bond
Arrows
Orbitals
Bold Bond
Bold Wedged Bond
Hollow Wedged Bond
Wavy bond
Table
Drawing Elements
Brackets
Query tools
TLC plate
Chemical Symbols
Templates
Cyclopropane Ring
Cyclobutane Ring
Cyclopentane Ring
Cyclohexane Ring
Cycloheptane Ring
Cyclooctane Ring
Acyclic Chain
Cyclohexane chair 1
Cyclopentadiene Ring
Cyclohexane chair 2
Benzene Ring
Optional Toolbars
ChemDraw provides a number of optional toolbars
and information windows to facilitate production of
ChemDraw documents. These toolbars are accessed
from the View menu. They are divided into three
basic groups:
CambridgeSoft
Optional Toolbars
Templates
To dock a toolbar:
standard
toolbars
information
windows
To undock a toolbar:
tool
palettes
templates
ChemDraw 8
ChemDraw
Administrator
Shows
Pointer:
X/Y
Pointer:
dX/dY
Selection:
X/Y
W/H
position of a selection
width/height of a selection
Angle:
Dist:
Periodic Table
The Periodic Table window displays a floating
periodic table. It can be used both for reference and
to insert elements into structures.
10
CambridgeSoft
Optional Toolbars
ChemDraw
an existing
labeled
atom
an empty
space
Character Map
The floating Character Map window displays the
256 ASCII characters in any font. The default font is
Symbol. Use it to add symbols or styled fonts to
labels.
ChemDraw 8
11
Administrator
Customizing ChemDraw
Setting Preferences
Preferences affect the way the ChemDraw
application works, regardless of the document with
which you are working.
To open the Preferences dialog box:
From the File menu, choose Preferences.
The Preferences dialog box appears:
12
CambridgeSoft
Customizing ChemDraw
ChemDraw 8
13
ChemDraw
4. Click Save.
3. Click Open.
Administrator
No
Using Documents
Documents are the ChemDraw workspace where
you create and manipulate structures. You can create
a new document or open an existing document and
edit it.
14
Creating a Document
You can create a new, blank document using the
ChemDraw default settings, or use a Style Sheet or
Stationery Pad with customized settings.
the list.
CambridgeSoft
Using Documents
Opening a Document
To open a document:
minutes to use.
Undoing Actions
To undo the last action performed:
From the Edit menu, choose Undo.
ChemDraw 8
15
ChemDraw
Administrator
Saving Documents
Redoing Actions
When you undo an action, the Redo command
becomes active so you can reverse the effect of the
Undo command.
To redo the last action undone:
From the Edit menu, choose Redo.
The last action undone is reinstated. The Undo
command changes to reflect that action. The
Redo command changes to reflect the next
action that can be redone.
Repeating Actions
If an action is repeatable, the name of the action
appears next to the Repeat command on the Edit
Menu.
To repeat an action:
From the Edit menu, choose Repeat.
The last action performed is repeated.
16
CambridgeSoft
Using Documents
document.
3. Type a new file name.
4. Click Save or OK.
ChemDraw 8
17
ChemDraw
Administrator
Closing a Document
To close a ChemDraw document:
From the File menu, choose Close.
If the document contains unsaved information, you
are prompted to save the file.
Accessing Documents
Quickly
You can access ChemDraw documents quickly by
placing them in the ChemDraw Items folder and
then selecting them from the Open Special menu.
You can access open documents quickly by using
the Window menu.
4. Click OK.
18
CambridgeSoft
Accessing Documents Quickly
Printing
ChemDraw 8
19
ChemDraw
Administrator
Include PostScript
Scripts (Macintosh)
Closing ChemDraw
20
CambridgeSoft
Scripts (Macintosh)
Chapter 2: Tutorials
ChemDraw
Overview
1. Start ChemDraw.
2. From the File menu, choose Save As.
3. Type tut1.cdx in the appropriate text box.
4. Select a folder in which to save the file.
5. Click Save.
6. From the View menu, choose Show General
Toolbar.
7. From the View menu, choose Show Info
Window.
Tutorial 1: Reaction
Schemes
In this tutorial, you will draw the following
(simplified) reaction scheme:
OH
4-hydroxy-4-methyl-2-pentanone
1 mole
2-propanone Rx 60%
ChemDraw 8
Chapter 2: Tutorials
Tutorial 1: Reaction Schemes
21
Administrator
Create a bond:
1. Click the Solid Bond tool
22
Chapter 2: Tutorials
CambridgeSoft
Tutorial 1: Reaction Schemes
ChemDraw
isobutene
w/textbox
100%
4. Drag the Selection Rectangle to the right.
3. Type an uppercase O in the text box that
appears.
.
following:
Click in an empty area of the window.
Click another tool.
Next, you duplicate a structure and then create
another structure from the duplicate.
Duplicate the structure:
1. Click the Lasso tool
ChemDraw 8
Chapter 2: Tutorials
Tutorial 1: Reaction Schemes
23
Administrator
OH
In the following steps, you use a different method
for selecting structures and then separate the
structures to make room for an arrow.
O
1. Click the Marquee tool
2. Type O or o.
palette.
OH
When you use HotKeys that represent a single
element, the correct number of hydrogen atoms is
added to the label.
Align the structures:
1. Select the structures.
2. On the Object menu, point to Align, and then
choose T/B centers.
row.
24
Chapter 2: Tutorials
CambridgeSoft
Tutorial 1: Reaction Schemes
button.
OH
OH
4. Type OH.
mouse button.
O
O
OH
OH
OH
ChemDraw 8
SelectMinus
Chapter 2: Tutorials
Tutorial 1: Reaction Schemes
25
ChemDraw
Administrator
O
OH
OH
OH
O
OH
flush left.
To group objects:
1. Click a Selection tool, the Lasso
Marquee
.
or
4. From the Text menu, choose Centered.
26
Chapter 2: Tutorials
CambridgeSoft
Tutorial 1: Reaction Schemes
2-propanone
2. Press Enter or Return to insert a new line.
2-propanone
3. Type 2 moles.
2-propanone
2 moles
drawing elements.
O
3. Point to the upper left corner of the reaction
2-propanone
2 moles
ChemDraw 8
Chapter 2: Tutorials
Tutorial 1: Reaction Schemes
27
ChemDraw
Draw a ring:
pentanone 60%
Administrator
OH
Cyclohexane cursor
OH
appears.
4-hydroxy-4-methyl-2-pentanone
1 mole
2-propanone
2 moles
Tutorial 2: Drawing an
Intermediate
OOH
Add a bond:
1. Click the Solid Bond tool
28
Chapter 2: Tutorials
CambridgeSoft
Tutorial 2: Drawing an Intermediate
another bond.
the outside.
The bond moves to the inside on the first click
and to the outside on the second click
b. Hold the mouse button and drag diagonally
ChemDraw 8
Chapter 2: Tutorials
Tutorial 2: Drawing an Intermediate
29
ChemDraw
3. Type OH.
Administrator
OOH
mouse button.
OOH
arrowhead to appear.
OH
O-
30
Chapter 2: Tutorials
CambridgeSoft
Tutorial 2: Drawing an Intermediate
OOH
ChemDraw
5. Click Save.
Create a ring:
1. Click the Cyclohexane Ring tool
O-
OH
ChemDraw 8
Chapter 2: Tutorials
Tutorial 3: Using Rings
31
Administrator
ring.
32
Chapter 2: Tutorials
CambridgeSoft
Tutorial 3: Using Rings
ChemDraw
the bonds.
ChemDraw 8
Chapter 2: Tutorials
Tutorial 3: Using Rings
33
Administrator
CH
34
Chapter 2: Tutorials
CambridgeSoft
Tutorial 3: Using Rings
Tutorial 4: Fischer
Projections
Glucose
HO70%
OH
H
OH
OH
ChemDraw 8
Chapter 2: Tutorials
Tutorial 4: Fischer Projections
35
ChemDraw
Administrator
perpendicular bond.
Add horizontal bonds to the second atom in the
string of bonds you created:
Point to C2 and click the atom to add a
perpendicular bond.
36
Chapter 2: Tutorials
CambridgeSoft
Tutorial 4: Fischer Projections
ChemDraw
3. Point to C6.
ChemDraw 8
Chapter 2: Tutorials
Tutorial 4: Fischer Projections
37
CHO
Administrator
CH2OH
4. Double-click C6 to create a text box, then type
CH2OH.
for hydrogen.
CHO
CHO
H
CH2OH
shown below.
CHO
H
38
Chapter 2: Tutorials
CambridgeSoft
Tutorial 4: Fischer Projections
CHO
H
shown below.
OH
H
ChemDraw
HO
CHO
H
Fischer
H OGlucose
OH
OH
OH
H
70%
CH2OH
OH
OH
C H 2O H
C6H12O6
Exact Mass: 180.06
Mol. Wt.: 180.16
m/e: 180.06 (100.0%), 181.07 (7.1%), 182.07 (1.4%)
C, 40.00; H, 6.71; O, 53.29
Tutorial 5: Perspective
Drawings
In this tutorial you will learn how to create a
perspective drawing by drawing the following
-D-glucose as a Haworth projection.
CH2OH
O
OH
OH
OH
OH
ChemDraw 8
Chapter 2: Tutorials
Tutorial 5: Perspective Drawings
39
Draw a ring:
1. Click the Cyclohexane Ring tool
Administrator
3. Type o.
40
Chapter 2: Tutorials
CambridgeSoft
Tutorial 5: Perspective Drawings
ChemDraw
4. Point to C1 again.
O
below.
O
For the downward bond for C5, you must turn Fixed
Lengths off or the bond will be joined to the upward
bond of C3.
You can temporarily disable Fixed Lengths using a
modifier key:
1. Point to the atom shown below.
ChemDraw 8
Chapter 2: Tutorials
Tutorial 5: Perspective Drawings
41
Administrator
Resize handle
OH
OH
OH
OH
OH
42
Chapter 2: Tutorials
CambridgeSoft
Tutorial 5: Perspective Drawings
CH2OH
O
OH
OH
OH
OH
OH
OH
OH
OH
OH
OH
OH
CH2OH
O
OH
OH
CH2OH
O
OH
CH2OH
O
OH
OH
OH
OH
ChemDraw 8
Chapter 2: Tutorials
Tutorial 5: Perspective Drawings
43
ChemDraw
OH
CH2OH
O
OH
Tutorial 6: Newman
Projections
Administrator
5. Click Save.
44
Chapter 2: Tutorials
CambridgeSoft
Tutorial 6: Newman Projections
fragment.
4. Release the mouse button when the highlight
ChemDraw 8
Chapter 2: Tutorials
Tutorial 6: Newman Projections
45
ChemDraw
Administrator
Tutorial 7: Showing
Stereochemistry
This tutorial demonstrates using Stereochemistry
markers and the flip command.
Create a new document.
1. From the File menu, choose New Document.
2. From the File menu, choose Save As.
3. Type tut7.cdx in the appropriate text box.
4. Select a folder in which to save the file.
5. Click Save.
OH
NH2
46
Chapter 2: Tutorials
CambridgeSoft
Tutorial 7: Showing Stereochemistry
NH2
NH2
Marquee.
2. From the Object menu, choose Show
Stereochemistry.
ChemDraw 8
Chapter 2: Tutorials
Tutorial 7: Showing Stereochemistry
47
ChemDraw
Administrator
(S)
OH
NH2
NH2
HO
(R)
(R)
48
Chapter 2: Tutorials
CambridgeSoft
Tutorial 7: Showing Stereochemistry
Overview
ChemDraw provides the following tools for drawing
chemical structures:
Bond tools.
Ring tools.
Text tools.
An acyclic chain tool.
Automatic error checking.
Drawing Settings
Drawing settings are document settings that affect
how bonds and other objects are drawn. You can
configure the drawing settings for an entire
document or for a particular object as follows:
For the entire document, use the Document
Settings dialog box.
For an object, use the Object Settings dialog
box.
Changes made to the drawing settings affect the
active document window only. Drawing settings can
be saved in Style Sheets or Stationery Pads.
To apply settings from other documents to your
document, select Apply Document Settings
from... from the File menu.
ChemDraw 8
If you want to
Bond
Spacing
10%
14%
18%
49
ChemDraw
Administrator
Adjust
this
If you want to
Adjust
this
If you want to
Fixed
Length
Margin
Width
2 Point
Line Width
1 Point
2 Point
4 Point
8 Point
Color
Units
8 Point
0.5 Point
50
4 Point
1.5 Point
CambridgeSoft
Drawing Settings
If you want to
Atom and
Bond
Indicators
settings.
ChemDraw
Adjust
this
ChemDraw 8
51
Multiple Bonds
The Multiple Bond tool on the Main toolbar
includes the following palette.
Administrator
Tautomeric
Aromatic
Drawing Bonds
Double Either
Dative
Solid Bond
Triple
Multiple Bonds
Quadruple
Dashed Bond
Hashed Bond
Hashed Wedged Bond
Bold Bond
Double Bonds
There are three ways to draw a double bond:
Wavy Bond
52
CambridgeSoft
Drawing Bonds
.
.
Triple Bonds
You can draw any bond length and create any angle
relative to the X-axis. The Info Window displays the
bond length and angle as you drag the bond.
However, you can draw bonds that are constrained
to:
A fixed length
1. Click any bond tool.
to the other.
Quadruple Bonds
To draw a quadruple bond select the quadruple bond
tool from the Multiple Bonds palette, or:
1. Click any bond tool.
2. Drag from one end of an existing triple bond to
the other.
The triple bond changes to a quadruple bond.
ChemDraw 8
53
ChemDraw
bond.
Administrator
document window.
4. Move the end of the bond to other angles.
54
CambridgeSoft
Drawing Bonds
Drawing Rings
Cyclopropane
Cyclobutane
Cyclopentane
Cyclohexane
Cycloheptane
Cyclooctane
Drawing a Ring
If Fixed Lengths is on when you draw a ring, the
length of each bond in the ring is automatically set
to the fixed length. If Fixed Angles is on, the angle
the first bond in the ring makes with the X-axis is
restricted to 15-degree increments. For more
information, see Drawing Constrained Bonds on
page 53.
To draw a ring:
ChemDraw 8
bond.
55
ChemDraw
Administrator
tools.
2. Click+drag in the structure to the orientation
you want.
Vertical Orientation
Drawing Resonance
Delocalized Rings
If you click a bond, the ring is fused to that bond.
56
CambridgeSoft
Drawing Rings
Drawing Chains
To draw an acyclic chain:
1. Click the Acyclic Chain tool.
2. Drag in the direction you want the chain to grow
ChemDraw 8
in a document window.
57
ChemDraw
Administrator
Adding Chains
the chain.
grow.
Editing Bonds
You can modify the appearance of chemical
structures by:
Changing bond types
Changing bond alignment and orientation
document window.
Moving atoms
Layering bonds
Changing the bond order
4. Click Add.
58
CambridgeSoft
Editing Bonds
ChemDraw
CO2H
HO
CH3
The dative or wedged bond is changed to the
opposite orientation.
CO2H
HO
H
CH3
Centered
To change the alignment of a double bond:
1. Click the bond tool used to create the existing
Changing Orientation of
Wedged and Dative Bonds
When you draw or change a bond to a wedged or
dative bond, the orientation of the bond is chosen
appropriately.
double bond.
2. Do one of the following:
ChemDraw 8
59
Moving Atoms
Administrator
60
CambridgeSoft
Editing Bonds
Control-click.
2. Choose the appropriate bond type from the
Automatic Warnings
ChemDraw automatically checks for correct
chemical syntax as you draw. If ChemDraw finds a
potential problem, a red box is displayed around the
questionable object. The red box is displayed on
screen only and does not print.
To enable the automatic display of chemical
warnings:
On the View menu, choose Show Chemical
Warnings.
This setting applies to all documents.
ChemDraw 8
61
ChemDraw
Administrator
Automatic
DrawingStructures
from Chemical Names
Ultra
Converting Names to
Structures
You can insert a name as a structure in the document
window by using the
Insert Structure dialog box
Paste Special command
Insert Structure
For example, to insert 2-bromobenzoic acid:
1. From the ChemDraw Ultra Structure menu,
choose Convert Name to Structure.
Coordination complexes
Polyboranes
Polymers
Some highly-bridged ring systems, including
fullerenes and porphyrins/porphines
Some stereochemistry designators: +, -, +/-, +-,
D, L, DL, endo, exo, syn, anti, r, t, c
Although some trade names are supported,
Name=Struct is not intended to interpret trade or
common names. A chemical database, such as
chemfinder.com, is more appropriate for obtaining
structures for trade or common names.
62
CambridgeSoft
Automatic DrawingStructures from Chemical Names
Br
O
OH
2-bromobenzoic acid
Converting Captions to
Structures
If a caption is already present in the drawing area
you can convert it to a structure as follows:
1. Select the caption.
Paste Special
The Paste Special command allows you to paste
names copied to the clipboard from other
applications as a structure in ChemDraw.
ChemDraw 8
63
ChemDraw
Administrator
64
CambridgeSoft
Automatic DrawingStructures from Chemical Names
Creating Text
ChemDraw enables you to create the following
types of text:
Caption textCreate annotations, chemical
names, chemical formulas, page titles, and
information in tables.
OH
Phenol
ChemDraw 8
Caption Text
Atom Label
Text
65
ChemDraw
option:
Administrator
To change the
default for
Atom Label text
Caption text
Select
Require Alt+Enter or
Option+Return to Create
New Line in Atom
Labels.
Require Alt+Enter or
Option+Return to Create
New Line in Captions.
3. Click OK.
Formatting Text
Text settings affect how captions and atom labels for
the current document are drawn and formatted.
Formatting options include:
Font (font type)
Size (font size)
Style (font and baseline style)
Line spacing
Alignment
These options are described in the following
sections.
66
CambridgeSoft
Formatting Text
ChemDraw
Marquee tool.
2. On the Object menu, click Object Settings.
Captions
You specify the caption justification and line
spacing on the Captions tab of the Object Settings
dialog box. All text in a single caption must have the
same Justification and Line Spacing.
There are four available justifications:
Flush Leftcreates left-justified caption text.
Aligning Text
ChemDraw 8
67
Atom Labels
Administrator
NCH3
Stacked Above
N
CH2
OMe
Flush Left
RNH
Centered
N
CH2
OMe
Flush Right
Automatic Alignment
When you justify Atom labels automatically,
ChemDraw breaks the label into tokens. A token
consists of an uppercase letter followed by any
numbers or lowercase letters. The first token is
68
CambridgeSoft
Formatting Text
document window.
A text box appears.
2. Set the text format in one of the following ways:
options.
ChemDraw 8
69
ChemDraw
N
CH3
Administrator
Coloring Text
You can color captions and atom labels before or
after they are typed, and as a whole or in part.
tool.
Creating Captions
The default format options of any new captions you
create are specified in the Captions tab of the
Document Settings dialog box. You may edit these
options at any time. The settings affect the current
document only.
To create a caption:
1. Click the Text tool
the text.
3. From the Color menu, choose a color.
3. Type a caption.
70
CambridgeSoft
Creating Captions
Editing a Caption
To open a caption for editing:
1. Click the Text tool
Resize handle
ChemDraw 8
71
ChemDraw
Ultra Adding
Chemical
Names
a name.
Administrator
Cyclohexane
Radicals.
Mixtures and other multicomponent systems.
72
2. Point to an atom.
CambridgeSoft
Adding Chemical Names
value.
3. Click OK.
4. The margin width is applied to all subsequent
highlighted text.
If all the text is not highlighted, and you want to
select all of the atom label:
From the Edit menu, choose Select All.
label.
Cl
0.278 pt
Cl
0.6 pt
ChemDraw 8
73
ChemDraw
Administrator
H3C
an atom.
A highlight box appears over the atom.
C
H2
74
CambridgeSoft
Labeling Atoms with HotKeys
Function
Delete
Deletes objects.
Hard-Coded HotKeys
You cannot edit hard-coded HotKeys. The following
table contains a list of hard-coded HotKeys:
HotKey
Function
Enter or
Return
space
Creating HotKeys
/ (slash)
= (equal)
. (period)
ChemDraw 8
Items folder.
75
ChemDraw
HotKey
To add a HotKey:
1. Add a new line and type the key you want to
use.
Administrator
2. Type a space.
3. Type the letters to associate with the HotKey.
Repeating an Atom
Label
You can repeat an atom label using the text, bond, or
ring tools.
To label several atoms with the same text using the
Text tool:
previous label.
To label several atoms with the same text using a
bond, ring, or Acyclic Chain tool:
1. Click the tool.
2. Triple-click an atom to repeat the previous
label.
Atom Numbering
76
CambridgeSoft
Labeling Atoms With a Bond or Ring Tool
ChemDraw
If you want to
show previously
assigned atom
numbers.
show a previously
assigned atom
number.
Then
Right-click, point to
Atom, and then click
A previously assigned
number is displayed.
6
1
Right-click, and
choose Show Atom
Number.
assign an atom
number
4
3
ChemDraw 8
77
Administrator
a value:
To position
by angle or by clock
by offset
horizontal and
vertical
at specified coordinates
absolute
horizontal and
vertical
78
CambridgeSoft
Using the Text Tool with the Lasso Tool
Press Ctrl+Alt+Tab or
Command+Option+Tab.
Press Ctrl+Alt+Tab or
Command+Option+Tab.
ChemDraw 8
79
ChemDraw
Administrator
80
CambridgeSoft
Using Bitmap Fonts When Available (Macintosh)
Overview
to draw orbitals.
to draw arrows.
to
to draw arcs.
TLC tool
to reproduce TLC
experiments.
You can use the tool palettes as extensions of the
Main Tool Palette, or you can tear them off and place
them anywhere on your screen.
button.
The palette appears.
2. Drag to select a tool type from the palette.
3. Release the mouse button over the tool you
want to select.
The selected tool is now displayed on the Main
Tools Palette.
To display a tools palette, do one of the following:
From the View menu, select Other Toolbars,
then select one of the palettes.
Click the tools icon and drag to the palettes
title bar. Release the mouse button over the title
bar.
The selected palette is displayed, and can be
dragged anywhere on the screen.
ChemDraw 8
81
ChemDraw
Background color
Sigma Orbitals
Shaded
Solid color
Administrator
You can modify the fill colors with the Color menu.
Display the Info window to view the orbitals length
and angle relative to the X-axis while you draw it.
You can constrain the length and angle of an orbital
by selecting Fixed Lengths and Fixed Angles on the
Object menu.
To draw a -orbital:
1. Hold down the mouse button over the Orbital
tool
and drag to select the -orbital tool
s-orbitals
The s-orbital tools are shown below:
To draw an s-orbital:
1. Hold down the mouse button over the Orbital
tool
and drag to select the s-orbital tool
centered.
3. Drag outward.
orbital is to be attached.
end.
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CambridgeSoft
The Orbital Tools Palette
to be attached.
p-orbitals
To draw a p-orbital:
1. Hold down the mouse button over the Orbital
tool
and drag to select the p-orbital tool
d-orbitals
The d-orbital tools are shown below:
to be attached.
To draw a d-orbital:
3. Drag from the orbital node to the wide end of
to be attached.
3. Drag from the center of the orbital to the wide
Hybrid Orbitals
The hybrid-orbital tools are shown below:
dz2-orbitals
The dz orbital tools are shown below:
2-
ChemDraw 8
83
ChemDraw
Administrator
will be attached.
3. Drag from the center of the orbital to the wide
end of a lobe.
Symbols 94 dpi
H-dot symbol
When you attach a symbol (other than H-dot or Hdash) to an atom, it remains at a fixed distance from
the central character of the atom label. If you drag
the symbol, it will maintain that fixed distance as it
moves around the atom.
84
Lone Pair
Use the lone pair symbol
to indicate a lone
pair of electrons common in Lewis structure
representations.
to
appear.
3. Drag from the charge portion of the symbol to
OH
Radical
Use the radical symbol
non-bonded electron.
to indicate a single
Charge Symbols
Use the charge symbols to represent charges on
structures.
To draw a charge and associate it with a structure:
1. Hold down the mouse button over the
Chemical Symbols tool
and drag to
to correspond.
ChemDraw 8
H2N
symbol to appear.
NH3
OH
85
ChemDraw
H3N
Administrator
OH
Attachment Points
The ability to indicate an attachment point is useful
in polymer-bound combinatorial synthesis, protein
chemistry, and other situations. ChemDraw has four
standard attachment point drawing tools that allow
you to indicate a point of attachment while
maintaining chemical meaning.
tool.
2. Drag the Rotation handle on the chemical
symbol.
For more information about rotating and resizing,
see Rotating Objects on page 101.
Arrows 94 dpi
Rotating a Symbol
Drawing an Arrow
To draw an arrow:
86
CambridgeSoft
The Arrow Tools Palette
Editing an Arrow
To lengthen, shorten, or rotate an arrow:
.
arrow.
Drawing Boxes
To draw a box:
1. Select one of the box tools.
ChemDraw 8
located.
3. Drag from one corner of the box diagonally to
be located.
3. Drag outward from the center.
87
ChemDraw
Drawing Lines
Lines drawn with the line tool differ in two
significant ways from bonds drawn with the bond
tools:
They are not included in chemical interpretation
of the drawing
Lines that cross appear solid
To draw using a line tool:
1. Select a line tool.
drawing element.
A highlight box appears.
3. Drag the object to the new size or orientation.
88
end.
CambridgeSoft
The Brackets Tools Palette
ChemDraw
Arcs 94 dpi
2. Point where you want a corner of the bracket to
be located.
3. Drag from one corner of the box diagonally to
Drawing Arcs
Where you access the arc tools depends on which
version of ChemDraw you are using.
Drawing Daggers
To draw an arc:
To draw a dagger:
1. Do one of the following:
1. Select a dagger tool.
Framing Objects
You can enclose your drawings or group structures
with a rectangle, brackets, parentheses, or braces.
Editing Arcs
To resize or rotate an arc using the Arc tool:
1. Select the Arc tool.
2. Press Shift and point to the clockwise end of the
arc.
ChemDraw 8
89
Administrator
Customized orbitals
Geometric shapes
Unique arrows
tool.
90
CambridgeSoft
The Pen Tool
ChemDraw
point.
Editing a Curve
You can edit a curve by selecting it and manipulating
it with the direction lines.
To select an existing curve:
1. Select the Pen
Direction Line
tool.
tool.
curve to appear.
3. Click to deposit an anchor point.
ChemDraw 8
91
Administrator
want.
Deleting a Segment
To delete a curve segment:
In the edit mode of the Pen tool, Alt+Shift+click
or Option+shift+click the control point where
you want to delete a curve segment.
The cursor appears as the Eraser tool before you
click.
Adding a Segment
To extend an existing curve by adding a segment:
1. Select the Pen tool and click the existing curve
appears as a hand.
selection tool.
2. From the Curves menu, choose a style.
92
CambridgeSoft
The Pen Tool
Shaded Style
You can apply shading to any curve, however the
shaded style works best with convex or slightly
concave shapes. Shading may not appear as desired
in extremely concaved shapes.
then...
front line.
Plain Style
To remove all styles from a curve:
With a curve selected, choose Plain from the
Curves menu.
ChemDraw 8
93
ChemDraw
Administrator
Add, delete or
duplicate a lane.
then...
1. Position the cursor on
then...
1. Right-click or Controlclick on a spot.
2. Choose the style or
color.
2. Right-click or Controlclick in the plate.
action.
NOTE: You can also delete
lanes with the Eraser tool.
Move a spot.
Enlarge or smear
a spot.
Ctrl+drag or Option+Drag
the spot.
Delete a spot.
1. Cross arrows
used
to enlarge a spot.
2. Horizontal arrow
3. Vertical arrow
Rf Display
When you select Show Rf, a text label appears near
the spot showing the spot's retention factor value. By
default, the tag will show the Rf to two decimal
places. You can change the tag as follows:
94
CambridgeSoft
The TLC Tool
Select the tag with the Text tool and edit the Rf
value.
Solvent front
Spot
Enlarged spot
Widened spot
Resizing Spots
Elongated spot
ChemDraw 8
Origin
Lanes
95
ChemDraw
Administrator
96
CambridgeSoft
The TLC Tool
other object.
or other objects.
ChemDraw 8
97
ChemDraw
Overview
Administrator
tool and
98
CambridgeSoft
Using a Selection Tool
Press Esc.
Select a different tool.
Select another object without holding down
Shift.
The selected objects are deselected.
If the chemical structure or other object is part of a
group, the entire group is selected. For more
information, see Grouping Objects on page 106.
Deleting Objects
To delete selected objects, do one of the following:
Press Delete.
Press Backspace.
From the Edit menu, choose Clear.
Moving Objects
To move an object:
1. Select the object using a selection tool.
2. Point within the border of the Selection
rectangle.
3. Click and drag the object.
ChemDraw 8
99
ChemDraw
Administrator
Pasting
To paste a copy of the contents of the Clipboard into
a document window:
1. Click a Selection tool.
2. From the Edit menu, choose Paste.
Moving Atoms
You can move the atoms within a chemical structure
using a selection tool.
To move a single atom:
1. Point to an atom using a selection tool.
Cutting
To use the clipboard:
100
CambridgeSoft
Using a Selection Tool
Duplicating Objects
To duplicate objects with a selection tool:
1. Click a selection tool.
2. Select the objects.
Rotating Objects
To rotate objects:
1. Select the objects to rotate using a selection
tool.
3. Ctrl+drag or Option+drag to create a copy and
position it.
Rotation handle
counterclockwise.
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101
ChemDraw
Administrator
Structure Perspective
NOTE: Captions and atom labels that contain
multiple colors change to the foreground color when
rotated. However, all colors contained in the
captions are printed.
To rotate the selected objects a specified number of
degrees:
Trackball tool.
2. Place the cursor inside the marked rectangle
Y axes only.
You can also select part of a complex molecule and
rotate it around a particular bond.
2. Type a number and click degrees CW for a
clockwise rotation or degrees CCW for
counterclockwise rotation.
3. If you want to rotate the atom label text, click
Rotate Atom Labels.
4. Click Rotate.
102
Flatten Command
Although the Trackball tool is not intended to be a
3D modeling tool, it does introduce z-coordinate
information that is saved in .cdx files. This pseudo3D structure can be confusing when opening files
that have been saved after perspective manipulation.
CambridgeSoft
Structure Perspective
Tool.
Reflecting Objects
Through Planes
You can reflect structures through planes
perpendicular to the X-axis or Y-axis using a
selection tool. Used with duplicating, you can create
mirror images of chemical structures for
representing racemic mixtures and other
stereoisomers.
Flipping Objects
To reflect an object through a plane perpendicular to
the X-axis:
1. Select the objects to reflect.
Resizing Objects
You can resize objects by dragging the resize handle
of a selected object or by scaling. If all objects in the
document window are part of the selection, after you
resize, a message appears asking whether you want
to change the document settings for that document.
If you do so, all subsequent bonds, atom labels, and
captions are drawn using the new settings.
ChemDraw 8
103
ChemDraw
Administrator
Resize handle
you want.
The screen and Info window indicate the
percentage enlarged or reduced.
50%
Scaling Objects
To resize objects with the Scale command:
button.
104
CambridgeSoft
Resizing Objects
3. Click Scale.
ChemDraw
Distorting a Selection
In most cases, when you resize an object, the aspect
ratio of the object (the ratio of the height to width)
does not change. However, it is possible to change
the aspect ratio (distort) of certain objects including
chemical structures, circles, boxes, and ovals.
To distort an object in the horizontal or vertical
direction:
selected bonds
handle.
Joining Objects
Use the Join command in the Object menu to fuse
two chemical structures together. Once structures
are joined they can be easily selected by
double-clicking.
To join chemical structures along the length of a
bond:
1. Select a bond or atom in one of the molecules
ChemDraw 8
105
tool.
Administrator
Grouping Objects
You can group a number of objects drawn
separately. Grouping creates an association between
objects so they can be easily selected. You can select
all grouped objects by double-clicking with a
selection tool. Objects within a group can be
selected individually and manipulated while still
remaining part of the group.
If you want to group objects so that the individual
objects in the group cannot be accessed, you can
create an Integral group. When you select any object
in an Integral group, the entire group is selected.
Grouping does not lock the position or orientation of
objects. Grouped objects maintain their relative
positions when they are centered on the page,
aligned or distributed.
Atoms and bonds making up a single chemical
structure are always grouped. If you group part of a
structure with other objects, the resulting group
contains the entire structure. If you add atoms or
bonds to a grouped structure, the new atoms and
bonds are part of the group.
106
Ungrouping Objects
To ungroup objects that are grouped:
1. Select a group, as above.
2. From the Object menu, choose Ungroup.
CambridgeSoft
Grouping Objects
tool.
2. From the Object menu, choose Group.
ChemDraw 8
107
ChemDraw
Administrator
108
CambridgeSoft
Grouping Objects
Overview
ChemDraw provides advanced drawing features that
allow you to:
Label functional groups with Nicknames.
Contract and expand sections of structures.
Add bonds to specific characters in atom labels.
Applying Nicknames
To use a Nickname to label an atom:
1. Create a structure.
Using Nicknames
Nicknames allow you to create short names for
functional groups to use as an atom label or part of a
label. When an atom is labeled with a Nickname, the
chemical significance of the expanded structure is
retained.
NHOH
ChemDraw 8
NHOH
109
ChemDraw
Et
Administrator
110
CambridgeSoft
Using Nicknames
Element
Ac
Acetyl
Actinium
Am
Amyl
Americium
Np
paraNitrophenyl
Neptunium
Pr
Propyl
Praeseodymium
Troubleshooting Nicknames
If the command Define Nicknames is dimmed,
check for the following:
A connection point is not present
More than 2 connection points are defined
The connection point is not a single bond
In the example below, the functional group was
drawn and the entire group selected. Because there
is no atom that indicates a connection point, you
cannot define a Nickname.
incorrect definitions
ChemDraw 8
correct definitions
Gly Ala OH
111
ChemDraw
Symbol
Administrator
GlyAlaOH
3. Click Delete.
Contracting Labels
Viewing Nicknames
HGlyAlaOH
Deleting Nicknames
To delete a Nickname:
1. From the File menu, choose list Nicknames.
2. Select the Nickname that you want to delete
112
CambridgeSoft
Contracting Labels
molecule
Expanding Labels
If your structures contain defined nicknames, long
atom labels, or contracted labels, ChemDraw can
restore your structures to the fully expanded form.
Contracted Form
Ph
Multi-Attached Labels
Multi-attached atom labels enable you to draw
chemical structures more efficiently by allowing
you to attach bonds anywhere along an atom label.
H2
C
CH2 CH2CHCH3
CH2
CH3
NH
O
Expanded Form
CH3
Expanded structure
O
CH2CH2NHCCH3
ChemDraw 8
113
ChemDraw
atom label.
2. Select a Bond tool.
3. Position the cursor where you want to attach
additional bonds.
bonds.
Ph
CH2 CH2CHCH3
create a bond.
Using Multi-Center
Bonds
Pro
114
CambridgeSoft
Using Multi-Center Bonds
forward.
2. Select the downward bond.
3. Double-click on the cyclopentadienyl ring with
a selection tool.
The entire structure, including the single bond,
is selected. The Cp ring and the single bond are
associated as one structural unit because
ChemDraw recognizes the bond between them.
NOTE: For the best looking structure, you may
need to draw a longer than normal bond. You can
toggle the Fixed Length command by typing Ctrl +L
or Command+L.
Fe
Using Variable
Attachment Positions
Pro
Br
Br
Br
Br
Br
o-Dibromobenzene
ChemDraw 8
m-Dibromobenzene
p-Dibromobenzene
115
ChemDraw
Fe
Administrator
Br
Br
Br
Using Structure
CleanUp
Pro
Br
116
CambridgeSoft
Using Structure CleanUp
Cl
OH
O
HO
Before
After
Cl
ChemDraw 8
117
ChemDraw
Administrator
Coloring Objects
Any object that you can select with a selection tool
can be colored. You can color individual bonds, part
or all of a chemical structure, or objects such as
boxes, curves, arrows, orbitals and reaction
mechanism symbols.
The border of objects that are shaded or filled, such
as white filled s-orbitals in the Orbitals palette, are
the same color as the shading or fill. The border of
objects that are hollow, such as circles and hollow
boxes in the Drawing Elements palette can be
colored, but the inside of the object cannot.
To color an object:
1. Select the object in a document window with a
selection tool.
118
CambridgeSoft
Working with Color
Option
Description
Set Color
Description
New Color
ChemDraw 8
119
ChemDraw
Luminosity box
Administrator
5. Click OK.
120
CambridgeSoft
Working with Color
ChemDraw 8
121
ChemDraw
Removing Colors
Administrator
Choosing a Template
To choose a template from the Template palette:
1. Hold down the mouse button over the
Templates tool
.
Using Templates
When you draw with templates, the first bond drawn
determines the position of the template in a
document window. All remaining bonds are drawn
counterclockwise. The most nearly vertical bond on
the far-left atom is drawn first, from top to bottom.
If there are two equivalent bonds, the atoms that are
at a lower position are used to draw the first bond.
Drawing direction of template structures
122
CambridgeSoft
Drawing With Templates
Drawing a Template
To draw a template:
Template Panel
Resize
Handle
Pane
Drawing Area
ChemDraw 8
123
ChemDraw
Creating Templates
Administrator
Orientation of Templates
To make the templates that you create as easy to
draw with as possible, it is recommended that you
orient your structures so that the bond that
establishes the position of the template, for example,
the bond used for fusing is left and vertical. The
most vertical left bond is drawn first. For examples,
see Using Templates on page 122.
Template Panels
To increase the size of the Template panel:
Drag the Template dividing line.
To add a row of panes to the Template panel:
Templates2 250 dpi
124
and hold
CambridgeSoft
Drawing With Templates
to delete.
2. From the Edit menu, choose Delete Column.
ChemDraw 8
125
ChemDraw
delete.
Administrator
126
CambridgeSoft
Drawing With Templates
Checking Chemistry
The Check Structure command identifies valence
and label errors in your structure.
Check Structure
You can check the chemistry of a selected structure,
part of a structure, or caption (in Formula style) with
the Check Structure command. The structure is
checked using normal valences and elements, and
defined Nicknames.
ChemDraw 8
127
ChemDraw
Overview
Administrator
Property
Description
Formula
Viewing Analysis
Information
The Analysis window displays the chemical
formula, exact mass, molecular weight, m/e, and
elemental analysis for the entire document, a
structure, part of a structure, or a caption in Formula
style.
To view analysis information:
128
CambridgeSoft
Viewing Analysis Information
Description
m/e
Elemental
Analysis
HO
OH HO
O
HO
ChemDraw
Property
OH
glucose
C6H12O6
Exact Mass: 180.06
Mol. Wt.: 180.16
m/e: 180.06 (100.0%), 181.07 (7.1%), 182.07
(1.4%)
C, 40.00; H, 6.71; O, 53.29
Showing
Stereochemistry
When the Show Stereochemistry option is selected,
ChemDraw calculates the absolute stereochemistry
for tetrahedral atoms and double bonds according to
the Cahn-Ingold-Prelog (CIP) priority rules. For
more information about the CIP rules, see
Stereochemistry on page 8.
Only tetrahedral and double-bond stereochemistry
are supported, and only non-racemic
stereochemistry is interpreted. Stereochemical
indicators for aromatic bonds are not shown.
ChemDraw calculates and displays the following
stereochemical terms:
(R), (S)Standard tetrahedral stereochemistry
(r), (s)Tetrahedral stereochemistry
determined by other stereochemical centers.
For example: cis-decalin and myo-inositol.
(E), (Z)Standard double-bond
stereochemistry
The atom label settings determine the font style and
size of the terms.
ChemDraw 8
129
Administrator
Stereochemistry Indicators
Positioning Indicators
move.
2. Right-click and choose Position.
Cholesterol 60%
H
(S)
(S)
(R)
(S)
(S)
HO
(Z)
cholesterol
Hiding Indicators
To hide an individual indicator:
a value:
To Position
Removing Indicators
To delete an indicator:
1. Click the indicator.
2. Click the eraser tool and then click the
indicator.
130
at specified coordinates
absolute, horizontal
and vertical
CambridgeSoft
Showing Stereochemistry
Converting Structures to 3D
Chem3D opens.
ChemProperties
150 dpi
are finished.
The edited structure appears in the ChemDraw
document window.
Ultra Viewing
Chemical
Properties
ChemDraw Ultra, using an add-on,
ChemProp/Draw, calculates predicted values for the
physical and thermodynamic properties of a selected
structure of up to 100 atoms. You can view the
values in the Chemical Properties window.
ChemDraw 8
131
ChemDraw
Administrator
Boiling Point
Melting Point
Description
The boiling point for the
structure. Reported in Kelvin
at 1 atm.
The melting point for the
structure. Reported in Kelvin
at 1 atm.
Critical
Temperature
Critical Pressure
Critical Volume
Gibbs Energy
Henrys Law
132
Property
Description
Ultra CLogP
The calculated
n-octanol/water partition
coefficient (log Pow).
Ultra CMR
CambridgeSoft
Viewing Chemical Properties
Pro Mass
Fragmentation
Tool
ChemDraw
C3H6
42.047
C3H6
42.047
3. The Alt or Option key also allows you to turn
To fragment a structure:
C3H6
42.047
C3H6
42.047
C3H6
C2H4
28.0313
C4H8
56.0626
42.047
C3H6
42.047
ChemDraw 8
133
SpectrumStructure Assignments
Ultra
Administrator
Assigning Structures to
Spectra
Removing Spectral
Assignments
To remove spectrum to structure assignments:
1. Click the Lasso or Marquee tool.
2. Select the objects from which to remove the
assignment.
3. From the Structure menu, choose Clear
Spectrum-Structure Assignment.
10
PPM
134
CambridgeSoft
Spectrum-Structure Assignments
3.22
7.02
H6.39
7.02
7.18
ChemDraw
NMR Shift
Information
ChemNMR
Ultra
H
6.58
4
PPM
ChemDraw 8
Node
Shift
CH
7.02
CH
7.02
CH
7.18
CH
7.01
CH2
3.22
6.58
6.39
Base + Inc.
7.26
-0.12
-0.12
7.26
-0.05
-0.19
7.26
0.04
-0.12
7.26
-0.05
-0.20
1.37
1.22
0.63
5.25
1.65
-0.32
5.25
0.09
1.05
135
Administrator
136
CambridgeSoft
NMR Shift InformationChemNMR
ChemDraw 8
Atom Properties
To assign properties to selected atoms in a structure:
1. Do one of the following:
137
ChemDraw
Chapter 9:
Pro Drawing Query Structures
X3
T
*2HS
Administrator
R
S
Query Property
Substituents: Up to (followed by
the maximum number of
substituents)
Implicit Hydrogens
Unsaturation
Reaction Change
Reaction Stereo
Translation
Isotopic Abundance
138
CambridgeSoft
Atom Property Options
Substituents
Option
Search Result
Free Sites
Up to
Exactly
ChemDraw 8
Search Result
Default. Search is determined by
the target database. Some
databases (including ISIS) find
compounds with any substitution
at this atom and some databases
(including DARC) find only
compounds with substitution
exactly as drawn.
Implicit Hydrogens
The Implicit Hydrogens property specifies whether
additional, implicit hydrogen atoms may be attached
to the selected atoms. If implicit hydrogen atoms are
not allowed, all valences to that atom must be filled
139
ChemDraw
Administrator
Option
Search Result
Allowed
Search Result
Any
140
Option
Search Result
Simple ring
Fusion
Spiro or
higher
Unsaturation
The Unsaturation property specifies whether a
multiple bond is attached to the selected atoms. The
unsaturation options are described in the following
table.
Option
Search Result
Unspecified
CambridgeSoft
Atom Property Options
Reaction Change
Option
Search Result
May be
anything
Must be as
specified
Reaction Stereo
The Reaction Stereo property specifies that the
selected atoms are stereocenters in a reaction. This
property is only meaningful when searching a
database containing chemical reactions.
Option
Search Result
Retention
Translation
The Translation property specifies what is required
to match in the structure query and possible database
hits in a Markush DARC query.
The translation options are described in the
following table:
Option
Definition
Equal
Broad
Narrow
Any
Search Result
Any
Inversion
ChemDraw 8
Isotopic Abundance
The Isotopic Abundance property gives you the
ability to distinguish between different isotopic
compoundsfor example between mono- and hexadeuterobenzeneby specifying a nuclide at any
location.
141
ChemDraw
Administrator
Option
Search results
Unspecified Default
Any
Natural
Indicates an isotopically
unmodified nuclide.
Enriched
Indicates a mixture of
isotopically substituted and
isotopically unmodified
nuclides.
Deficient
Nonnatural
Indicates an isotopically
substituted nuclide, that is,
essentially all the molecules of
the compound have only the
indicated nuclide.
Abnormal Valence
The Abnormal Valence property specifies whether
selected atoms can have a valence other than
normal. Normal valences for each element are
defined in the Isotopes Table file in the ChemDraw
Items folder.
NOTE: The Abnormal Valence atom property does
not provide a visual indicator.
The Abnormal Valence options are described in the
following table.
Option
Search Result
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CambridgeSoft
Atom Property Options
Bond Properties
Indicator
Any
S/D
D/A
S/A
Rng
Topology: Ring
Chn
Topology: Chain
Rxn
Reaction Center
S/D
Any
S/D
S/D
Any
one bond
S/D
many bonds
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143
ChemDraw
Administrator
Option
Search Result
Double Either
Aromatic
Tautomeric
Triple
Quadruple
Any
S/D
D/A
S/A
Bond Types
This property specifies the bond type of the selected
bonds. The default bond type corresponds to the
current type of the bond (single, double, etc.) as
drawn.
The Bond Type options are described in the
following table.
Option
Search Result
144
CambridgeSoft
Bond Properties
Topology
The Topology property specifies the ring
environment of the selected bonds.
Search Result
Center
Make/Break
Change
Make&
Change
Not Center
Not Modified
Unmapped
Search Result
Unspecified
Ring
Chain
Ring or Chain
Reaction Center
The Reaction Center property specifies how the
selected bonds are affected in a reaction. This
property is only meaningful when searching a
database containing chemical reactions.
The Reaction Center options are described in the
following table
Option
Search Result
Unspecified
ChemDraw 8
Pro
3D Properties
145
ChemDraw
Option
Administrator
Option
Search Result
Exclusion
Sphere
Normal
Point
Centroid
Search Result
Angle
Dihedral
Distance
Line
Plane
146
CambridgeSoft
3D Properties
ChemDraw
indicator.
Racemic
Stereochemistry
Alternative
Group
Absolute
Stereochemistry
Relative
Stereochemistry
Query Indicators
move.
2. Right-click and choose Position.
ChemDraw 8
147
a value:
Administrator
To Position
at specified coordinates
absolute, horizontal
and vertical
tool.
Drawing
Stereochemical
Symbols
ChemDraw provides three types of stereochemical
flags that indicate that the molecule with which they
are associated represents one of the following:
RacemicA racemic mixture.
AbsoluteA pure enantiomer of known
configuration.
RelativeA pure enantiomer of unknown
configuration.
The font and size for stereochemical flags is
determined by the default Atom Label size for the
document.
To draw a stereochemical flag:
1. On the Query tools palette, click the tool for the
148
site number.
To decrement the number of free sites:
Hold the Alt or Option key while clicking the
atom.
You can also change the free sites by using the Atom
Properties dialog box or the shortcut menu. For
more information see Atom Properties on page
137.
Generic Nicknames
Generic nicknames represent a class of elements or
structural moieties. For example:
M can be a generic nickname for all metals
X can represent halides
Ary can represent an aromatic substructure
If you are using a query system that recognizes
generic nicknames, you can use these nicknames in
your ChemDraw query structure.
CambridgeSoft
Drawing Stereochemical Symbols
Element Lists
You can define your search query more concisely
with the element list. By labeling an atom position
as a list of elements you specify that one of these
elements must match in the structure for which you
are searching. The elements in the element list must
be separated by commas. A space after each comma
and brackets are optional. An example of an element
list is shown below.
[S,Se,Te]
NOTE: An element list may contain only atomic
symbols, plus D (deuterium) and T (tritium).
To create an element list:
1. Open an atom label text box.
2. Type an open bracket ([) followed by a list of
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149
ChemDraw
[Br, I, Cl]
Administrator
For example:
NO T F,Cl,B r,I
atom.
b. Not necessarily carbon (a generic nickname).
c. The bond type between the chalcogenide and
NOT[F,Cl,Br,I]
[- C, O, N]
[NOT C,O,N]
(a)
(b)
A
S/D
Link Nodes
(c)
The A label indicates that the atom may match any
atom except hydrogen. The mark near the bond
indicates that the bond has special properties. The
bond type specified in the Bond Properties dialog
box must be single or double, S/D. The [S,Se,Te]
specifies that one of these elements must match in
the target structures.
Element Not-Lists
The element not-list specifies that the elements in
the list match must not match in the structure for
which you are searching. Commas must separate the
elements in the element not-list. A space after each
comma and brackets are optional.
150
CambridgeSoft
Element Not-Lists
Properties.
[CH2]4-7
Representing Polymers
and Other Repeating
Units
Brackets, parentheses, and braces enclose structures
or structural fragments that are to be repeated a
number of times. The bracket properties in
ChemDraw allow you to specify the context and
orientation of the repeating units.
To enclose structures with brackets:
1. Click the Bracket tool
brackets.
3.
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151
ChemDraw
Structure-based Polymer
Representations
Structure-based polymer representations enclose
only a portion or a structure within brackets. One or
more bonds cross each of the enclosing brackets.
The crossing bonds match up, making the
polymer structure more explicit.
You create a structure-based polymer representation
by enclosing a portion of a structure in brackets with
a bracket type of SRU (n). The subscript n is
recommended by IUPAC to notate structure-based
representations of unknown size, but you can edit
the text using the text tool.
Cl
mon
A structure-based representation of
poly(vinyl chloride) is shown below.
Cl
OH
OH
HO
HO
mer
mer
*
n
Source-based Polymer
Representations
co
152
CambridgeSoft
Representing Polymers and Other Repeating Units
O
O
OH
HO
ChemDraw
Na+
Na+
O-
-O
O
H
H
3
COOH
O
O
COOH
c1
c2
COOH
O
O
c3
COOH
c4
mix
ChemDraw 8
13
14
Repeat Pattern
For simple linear polymers, the repeating units may
connect head-to-tail or head-to-head (or their repeat
pattern might be a mixture or unknown). You can
also assign this property to brackets.
Because of its prevalence, the Head-to-Tail type is
assumed to be the default Repeat Pattern, and does
not receive any special annotation on the brackets,
as shown below.
153
F
O
*
hh
O
O
*
O
Administrator
eu
NH2
G
Flip Type
For ladder-type polymers (those polymers with two
connecting bonds on each side), there is a potential
ambiguity in the order of the connections. You can
assign the Flip Type property to resolve that
ambiguity. This property is appropriate only for
brackets with exactly two crossing bonds, and is
disabled in other cases.
Because of its prevalence the No Flip type does not
receive any special annotation.
*
H
N
*
*
H
N
H
N
H
N
H
N
F
NH2
OH
OH
*
*
flip
H
N
H
N
*
*
N
H
N
H
Alternative Groups
You can create a search query that contains variable
functional groups or substructures. Instead of
submitting multiple queries on structures that share
a common substructure, you can submit a single
query with the parent structure. The parent structure
can have attachment points to a list of alternative
groups that you can define.
154
H
N
CambridgeSoft
Alternative Groups
Attachment
point symbol
ChemDraw
tool
R1
NH2
OH
ChemDraw 8
155
R1
NH2
NH2
R1
NH2
156
CambridgeSoft
Alternative Groups
R1
R1
NH2
Anonymous Alternative
Groups
An anonymous alternative group is a cross between
an element list and an alternative group. Element
lists are restricted to single elements, but
anonymous alternative groups can contain any
structure that can be represented by text. Nicknames
ChemDraw 8
[M,B,C]
[OCH3,OH]
X,S,Se
Atom-to-Atom Mapping
You can create correspondences between atoms in
different structures for use in creating queries for
searching a reaction database. The reactions mapped
can be single or multi-step. You can assign atom-toatom mapping for creating records for a reaction
database and for creating queries for searching a
reaction database. You can assign atom mapping in
two ways:
Automatic mapping, using the Map Reaction
Atoms command.
Manual mapping, using the Reaction
Atom-Atom Map tool
.
157
ChemDraw
OSiMe3
O
Rxn
Administrator
Ph
Rxn
Ph
OH
6
5
Automatic Mapping
2
example:
OSiMe3
O
6
1
Rxn
Rxn
Manual Mapping
Rxn
Rxn
Rxn
Rxn
4
3
+
Ph
Ph
158
CambridgeSoft
Atom-to-Atom Mapping
Export Compatibility
Rxn
7
OH
6
1
Rxn
Rxn
Rxn
OH
Rxn
7
2
Rxn
10
6
11
5
4
10
Rxn
11
5
4
Exported Query
Properties
ISIS
Mol
Rxn
Unspecified
Free Sites
Up to
Atom Properties
Substituents
to remove.
2. From the Structure menu, choose Clear
Reaction Map.
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ChemDraw
Exported Query
Properties
Administrator
Exactly
ISIS
Mol
Rxn
Xc
Xc
Xc
Exported Query
Properties
ISIS
Mol
Rxn
May be
anything
Any
Implicit Hydrogens
Not allowed
Must be as
specified
Allowed
Reaction Stereo
Inversion
No ring bonds
Retention
As drawn
Simple ring
Equal
Fusion
Broad
Spiro or higher
Any
Narrow
Unsaturation
Unspecified
Must be absent
Must be
present
Translation
Abnormal Valence
Not Allowed
Allowed
Bond Properties
Reaction Change
Bond Type
160
CambridgeSoft
Export Compatibility
Exported Query
Properties
Mol
Rxn
Single
Dashed
Hashed
Wedged
Hashed
Bold
Wedged
Wavy
Exported Query
Properties
ISIS
Mol
Rxn
Any
S/D
D/A
S/A
Unspecified
Ring
Chain
Topology
e
Hollow
Wedged
Dative
Unspecified
Double
Xg
Xg
Xg
Center
Make/Break
Change
Make&Change
Not Center
ChemDraw 8
h
X
i
X
Triple
Quadruple
Aromatic
Tautomeric
e
Reaction Center
Double Either
Double Bold
i
X
Xj
Xj
Xj
161
ChemDraw
ISIS
Exported Query
Properties
Administrator
ISIS
Mol
Rxn
Element Lists
Xko
Xko
Xko
Element NotLists
Xk
Xk
Xk
Alternative
Groups
Anonymous
Alternative
Groups
Link Nodes
Converted to Wedged
Xm
f Converted
Bracket
properties
Atom-Atom
mapping
p
X
hConverted
Converted to S/D
kTruncated
l
3D query properties
Converted to single.
Variable
Attachment
Positions
to Double
nConverted
p
a
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CambridgeSoft
Export Compatibility
Setting up Pages
You can create two types of documents:
PagesA single document containing one or more
sheets, each of which is printed on a single piece of
paper.
PostersA single large document, composed of as
many pieces of paper as necessary.
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ChemDraw
Overview
Size section.
Administrator
8.5"
1"
1"
11"
1"
6. Click OK.
164
CambridgeSoft
Setting up Pages
Type
1. From the File menu, choose Page Setup.
file name
&f
page number
&p
date printed
&d
time printed
&t
Type
centered
&c
right
&r
left (default)
&l
Page Setup
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ChemDraw
Administrator
Paper Type
Dimensions
US Letter
8.5 x 11 inches
US Legal
8.5 x 14 inches
A4 Letter
21 x 29.7 cm
B5 Letter
17.6 x 25 cm
Tabloid
11 x 17 inches
International
8.5 x 12 inches
Computer
14 x 11 inches
Page Orientation
To choose the orientation of the page:
Click the vertical (portrait) or horizontal
(landscape) orientation button.
The orientation of a document window changes
to the orientation you have chosen. This is
evident when the rulers are visible.
Reduce or Enlarge
Some printers include an option to reduce or enlarge
your drawings by a variable percentage (25-400%).
This option scales all objects and text in the
document window by the percentage specified. This
is not a change in magnification. The size of objects
is changed relative to the paper size, margins, and
orientation you have specified.
166
CambridgeSoft
35mm Slide Boundary Guides
Changing Perspectives
You can use a close-up view of objects in your
reaction scheme to make sure they are properly
positioned. At times, you may want to reduce your
view so that you can move groups of objects around
the page. You can change the magnification to
perform these functions by using the Magnify and
Reduce commands in the View menu, the Zoom
tool, or the magnification controls.
Magnify
ChemDraw 8
Actual Size
To return to the actual size from any other
magnification:
From the View menu, choose Actual Size.
The view is returned to the original size.
Reduce
To reduce the magnification:
1. Select an object around which you want to
Windows
Macintosh
Macintosh
Fit to Window
Fit to Window reduces the magnification until the
entire page is visible in the document window.
To view the entire drawing area in a document
window at once:
From the View menu, choose Fit to Window.
167
ChemDraw
Administrator
Showing Rulers
To display the rulers:
From the View menu, choose Show Rulers.
A check mark appears next to the Show Rulers
command, and the rulers appear along the top
and left edges of a document window.
Arranging Objects
Ruler Guides
Using Rulers
You can use the rulers to position objects a measured
distance away from some reference point or create
objects of an approximate size. The units used for
the ruler are set in the Preferences dialog box, where
you have the choice of inches, centimeters or points.
168
CambridgeSoft
Arranging Objects
Ruler Guides
ChemDraw
Hiding Rulers
To Hide the rulers:
intersect.
When the pointer is near to the center of the
Crosshair, it changes to an arrow.
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169
Administrator
Aligning Objects
Use the Align commands to align objects relative to
each other. Examples of the types of alignments are
shown on the menu.
Centering on a Page
To center an object (or group of objects) at the center
of the page:
2. From the Align submenu, choose one of the
1. Select the object you want to center using a
Align commands.
selection tool.
2. From the Object menu, choose Center on
Page.
170
CambridgeSoft
Arranging Objects
Send to Back
To place one object behind another within a layer:
1. Select the object that you want to send to the
Distributing Objects
Use the distribute commands to distribute objects
horizontally or vertically and at an equal distance
apart. For reactants and products with different
shapes, select the parts of the objects to distribute.
To distribute 3 or more objects:
1. Select the 3 or more objects to distribute.
H
OH
CH2Br
Bring to Front
To place one object in front of another within a
layer:
ChemDraw 8
forward.
171
ChemDraw
Pro
Creating Tables
Administrator
.
2. Do one of the following:
172
CambridgeSoft
Creating Tables
ChemDraw
OH
rows or columns.
customize.
5. Click OK.
If you want to
OH
Then choose
ChemDraw 8
173
If you want to
Then choose
on.
Administrator
NOTE: The style, font, and size that you set in each
column are maintained in all the rows that follow.
Compound
M.W.
tab
LogP
tab
LD50
tab
Compound
M.W.
LogP
LD50
tab twice
174
CambridgeSoft
Creating Tables
To move
Alt+Enter or Option+Return
down
Alt+Shift+Enter or
Option+Shift+Return
up
To move
Tab or Option+Tab
right
ChemDraw 8
175
ChemDraw
Use
Administrator
176
CambridgeSoft
Creating Tables
ChemDraw 8
OH
N[C@@H]1[C@H](O)CCCC1
177
ChemDraw
Overview
Administrator
C1=CC=CC=C1
c1ccccc1
C[1]CCCCC@1
178
Using Drag-and-Drop
You can use the drag-and-drop feature to copy
objects to place in other documents. To use this
feature in other applications, they must support
drag-and-drop. As when using the clipboard, the
information is transferred as a ChemDraw object
and can be edited.
You can also use the drag-and-drop feature to create
clipping files (Macintosh) or scrap files (Windows).
CambridgeSoft
Using Drag-and-Drop
Transferring Between
ChemDraw Documents
Whether you use the clipboard or drag-and-drop,
when you move objects into another ChemDraw
document they will behave in a well-defined way. In
particular, you should be aware of the behavior of:
Autoscaling
Bonds
All bonds drawn in the source document using the
values specified in the Drawing Settings dialog box
can be changed to use the Drawing Settings in the
destination document.
Any resized bond in the source document is scaled
in the destination document. The scale factor is
based on the ratio of the bonds length after resizing
(source) to the Fixed Length in the Drawing Settings
dialog box (source). This scaling process maintains
the source document proportions in the destination
document. All values in the Drawing Settings dialog
box are scaled using this method.
For example, the Fixed Length is set to 1.0 cm in a
source document. A benzene ring is resized in to
200%. The bond length is then 2.0 cm: a ratio of 2.0
cm:1.0 cm or a scale factor of 2. In the destination
document, the Fixed Length set to 1.7 cm. When the
benzene ring is pasted into the destination
document, the bonds are scaled by a factor of 2 to a
final bond length of 3.4 cm.
Bonds
Atom Labels
Atom Labels
Captions
ChemDraw 8
179
ChemDraw
Autoscaling
Administrator
Captions
180
CambridgeSoft
Transferring Between ChemDraw Documents
You can edit the reference number text with the Text
tool. If you have different types of reference text,
you are prompted to choose which type to continue
the sequence.
number.
ChemDraw tools and menus appear.
ChemDraw 8
session.
A number is added to the document.
181
ChemDraw
Embedding Objects
(Windows)
reference.
Administrator
reference.
When you add sequence numbers to sequential
drawings, the numbers increment automatically.
To insert a cross reference to an existing reference:
1. Double-click the structure associated with the
reference.
2. From the Edit menu, choose Insert Cross
Reference.
session.
A cross reference (default style: underlined
italic) is added to the diagram.
To navigate through the cross-references:
From the Edit menu, choose Go Forward or Go
Back.
182
Transferring PostScript
(Macintosh)
To obtain the highest quality drawings possible on a
PostScript printer, ChemDraw creates both a screen
representation and a PostScript representation of
your drawing. PostScript is a page-definition
language used to describe drawings. Many printers,
including most Apple LaserWriter printers, use
PostScript to create high quality output.
For best print quality under all circumstances, we
recommend that you leave the Include PostScript
and Include ChemDraw Laser Prep preferences
selected (default) when you copy and paste from
ChemDraw to other applications. The ChemDraw
Laser Prep option adds approximately 11K to 12K to
each drawing, but these options give you the greatest
flexibility if you give your document to someone
else or later want to print it on a PostScript printer.
CambridgeSoft
Edit Graphic Object (Macintosh)
ChemDraw 8
dialog box.
c. Click OK or Save.
183
ChemDraw
Connection Table
MSI MolFile
SMD
Administrator
File Formats
Bitmap (.bmp) Export Only
Bitmap (.bmp) files store raster graphics in an array
of individual bits. Bitmap images are the most
common format for continuous-tone images.
Because they represent a fixed number of pixels,
bitmaps are resolution dependent and may appear
jagged and lose detail if they are scaled on-screen or
printed on a higher resolution printer than they were
created for.
ChemDraw (*.cdx)
Other format options are noted in format
descriptions.
184
CambridgeSoft
Importing and Exporting
ChemDraw 8
185
ChemDraw
Administrator
186
CambridgeSoft
Importing and Exporting
ChemDraw 8
187
ChemDraw
Administrator
PICT (Macintosh)
PICT files contain a QuickDraw representation of a
ChemDraw drawing that can be used by various
drawing applications. You can save a ChemDraw
document in the PICT format so it can be opened by
one of these other applications. The PICT file format
contains ChemDraw structural information. PICT
files created by earlier versions of ChemDraw can
be reopened and edited by ChemDraw version 8.0.
However, the pictures contained in PICT files
created by versions of CS ChemDraw earlier than
version 3.5, or by other applications, are treated as a
single, non-editable, imported picture.
All colors are saved in the PICT file except for the
Background color.
188
CambridgeSoft
Importing and Exporting
ChemDraw 8
189
ChemDraw
Administrator
190
insert an
existing
graphic
Transferring ChemDraw
Documents Across
Platforms
Use the following procedures to transfer ChemDraw
documents across platforms. From the following
table, determine the versions of the ChemDraw
software between which you want to transfer
documents and then follow the appropriate
instructions.
CambridgeSoft
Transferring ChemDraw Documents Across Platforms
3.5x
3.x
To
Windows
Version
Instructions
4.0
4.0
4.0
3.x
3.5.x
= 3.x
Save as ChemDraw
3.x (.chm) and
follow the
instructions in
Transferring files
to ChemDraw/Plus
3.1 for the
Macintosh below.
To Mac
Version
Instructions
4.0
4.0
3.5.x
4.0
Save as ChemDraw
3.x (.chm).
ChemDraw 8
191
ChemDraw
Administrator
192
CambridgeSoft
Transferring ChemDraw Documents Across Platforms
ChemDraw
Finding Chemical
Suppliers on
ChemStore.com
Find Suppliers on ChemStore.Com opens the
ChemACX.Com page (ACXAvailable Chemical
Exchange) of the CambridgeSoft web site.
To access Lookup Suppliers on ChemStore.Com:
1. In ChemDraw, select the molecule for which to
search.
2. From the Online menu, choose Find Suppliers
on ChemStore.com.
Finding Information on
ChemFinder.com
Find Information on ChemFinder.com opens
ChemFinder.com, where you can search the
ChemFinder database for chemical information.
To access ChemFinder.Com:
1. In ChemDraw, select the molecule for which to
search.
2. From the Online menu, choose Find
Information on ChemFinder.com.
ChemDraw 8
193
Administrator
ACX Numbers
To Find an ACX number for a structure:
1. In a ChemDraw document, select the structure
ACX Structures
To find an structure that corresponds to an ACX
number:
1. From the Online menu, choose Find Structure
from ACX Number.
Browsing
ChemStore.com
Browse ChemStore.com opens the ChemStore page
of the CambridgeSoft web site.
To access Browse ChemStore.com:
From the Online menu, choose Browse
ChemStore.com.
The ChemStore.Com page opens in your
browser.
194
CambridgeSoft
Finding ACX Structures and Numbers
ChemDraw
Browsing
CambridgeSoft.com
Browse CambridgeSoft.com opens the Home page
of the CambridgeSoft web site.
To access the CambridgeSoft Home Page:
From the Online menu, choose Browse
CambridgeSoft.com.
The CambridgeSoft web site in your browser.
ChemDraw 8
195
Administrator
2. Click version of the manual to view.
Accessing
CambridgeSoft
Technical Support
Browse CS ChemDraw Technical Support opens the
Tech Support page of the CambridgeSoft web site.
To access CS ChemDraw Technical Support:
From the Online menu, choose Browse
CS ChemDraw Technical Support.
The Tech Support page opens in your browser.
Registering Online
Register Online opens the ChemClub page of the
CambridgeSoft web site, where you can register
your copy of ChemOffice.
To register online:
1. From the Online menu, choose Register
Online.
196
CambridgeSoft
Accessing CambridgeSoft Technical Support
ChemDraw 8
197
ChemDraw
Administrator
198
CambridgeSoft
Using the ChemOffice SDK
ChemDraw/Excel
CAMEO/Excel
CambridgeSofts version of CAMEO is an optional
plug-in for ChemDraw and ChemDraw/Excel.
CAMEO (Computer-Assisted Mechanistic
Evaluation of Organic Reactions) is a modular
expert system that predicts the products of organic
reactions, given starting materials, reagents, and
conditions. Originally developed at Yale University
as a standalone VAX application, it is now available
for Macintosh, Sun-Solaris, Linux and SGI/IRIX
ChemDraw 8
199
ChemDraw
Overview
Administrator
200
CambridgeSoft
CAMEO/Excel
ChemDraw/Excel
ChemDraw
Starting
ChemDraw/Excel
When you install ChemFinder, ChemDraw/Excel is
automatically installed.
To start ChemDraw/Excel:
From the Tools menu, select Add-Ins. In the
Add-Ins dialog box check the ChemDraw for
Excel checkbox and click OK.
A ChemOffice menu is added to the Excel
menu bar
medium.
4. Click the Trusted Sources tab and make sure
Importing Tables
ChemDraw/Excel allows you to import the
following types of files:
MDL SDFilesImports all records in the
database. Each molecule is given the name
stored in the SDFile. The molecules are stored
ChemDraw 8
ChemDraw/Excel
Starting ChemDraw/Excel
201
Administrator
Converting and
Updating a Worksheet
You can convert an existing worksheet into a
ChemDraw/Excel worksheet. You can do this
instead of copying and pasting information from a
worksheet into a ChemDraw/Excel worksheet.
You can also update an old ChemDraw/Excel
worksheet so that it has the same format as the new
ChemDraw/Excel worksheets.
To convert or update a worksheet:
From the ChemOffice menu, select
Convert/Update Worksheet.
The work sheet is converted or updated
appropriately.
Importing a Hitlist
To import a hitlist:
1. From the ChemOffice menu, select Get
ChemFinder List.
202
ChemDraw/Excel
CambridgeSoft
Converting and Updating a Worksheet
1. Click OK.
or click
Exporting Tables
1. Click Yes.
ChemFinder opens.
3. Open a database and perform a search.
or click
To export data:
1. Select the information to export:
If you want to export
Then
1. Click OK.
or click
ChemDraw 8
ChemDraw/Excel
Exporting Tables
203
ChemDraw
Error Messages
ChemDraw opens.
3. Draw the molecule in ChemDraw.
Administrator
molecule.
3. Type the file name and select the file type.
4. Click Save.
Adding Molecules
You can add molecules in all file formats supported
by ChemDraw to a spreadsheet. The names of added
molecules are retained. If the molecule does not
have a name, ChemDraw assigns the name:
Structure <n>, where n is a number unique to the
worksheet.
204
ChemDraw/Excel
CambridgeSoft
Adding Molecules
Saving Molecules
convert.
molecule structure.
2. From the ChemOffice menu, select Save
Molecule or click
.
convert.
NOTE: If you want to keep the original text,
copy it and paste it elsewhere. Note that this
command can also convert names generated
from Excel formulas.
3. From the ChemOffice menu, select Convert
.
Name To Molecule or click
Searching
You can perform the same types of searches in
ChemDraw/Excel as you can in ChemFinder:
Exact structure searching
Substructure searching
Similarity searching
Filter Tables
Filter tables allows you to search for exact structures
and substructures.
ChemDraw 8
ChemDraw/Excel
Saving Molecules
205
ChemDraw
Then
Administrator
or click
see the
click Restore Previous
previous query Query.
Then
4. Click Search.
search for a
structure
a. To load a structure,
right-click and select
Read Structure.
b. To edit the structure,
double-click it.
c. Select the Search
Type.
d. Select the Filter
Type.
search for a
formula
search for a
structure and a
formula
Similarity Searches
You can perform similarity searches to find
structures with features corresponding to your
search structure. For more information about
similarity searching, see the ChemDraw Webserver
Users Guide.
To search for similarity:
1. Select a cell containing the label Structure.
2. From the ChemOffice menu, select Similarity
.
Table or click
206
ChemDraw/Excel
CambridgeSoft
Searching
Naming Molecules
Excel recognizes certain characters as formulas. To
prevent the system from interpreting a molecule
name as an Excel formula, you can rename a
molecule.
To name a molecule:
1. Select the structure.
2. From the ChemOffice menu, select Name
.
Molecule or click
structure.
2. From the ChemOffice menu, select Paste
.
Molecule or click
Viewing Structures
ChemDraw/Excel allows you to select whether or
not to display structures in a cell. You can also adjust
the height and width of cells to display their entire
contents.
pictures.
2. From the ChemOffice menu, select Show
.
Picture or click
ChemDraw 8
ChemDraw/Excel
Working with Structures
207
ChemDraw
To hide structures:
1. Select the cells in which you do not want to
display pictures.
Administrator
Aligning Structures
A structure may fall outside the boundaries of its cell
because it is too big or because it is improperly
positioned within the cell. Use Align Pictures to
enlarge the cell or reposition the structure. If the
entire structure is within the cell, regardless of its
position, it is not affected by the Align Pictures
command. Always align pictures to the whole table.
To align structures:
1. Select the cells to align.
2. From the ChemOffice menu, select Align
Pictures or click
.
Resizing Structures
You can resize a single structure by click-dragging.
To resize multiple pictures use the Resize Picture
command.
NOTE: When pictures are resized larger than their
cells, use Align Pictures to enlarge the cells. Align
Pictures does not make cells smaller.
To resize pictures:
1. Select the chemistry cells whose pictures you
want to resize.
It is not necessary to only select chemistry cells.
Non-chemical cells or chemical cells without
pictures will be ignored.
208
ChemDraw/Excel
deselected.
Using ChemDraw/Excel
Functions
ChemDraw/Excel supplies nine functions that
return information about chemistry objects in a
specified cell. Seven of these functions take only
one argumentthe cell to which the function refers.
The remaining two functions may also take an
optional second argument as a string.
CambridgeSoft
Using ChemDraw/Excel Functions
Function
Action
ISSTRUCTURE
ISREACCTION
CHEM.FORMULA
CHEM.MOLWEIGHT
Returns molecular
weight for molecule in
cell reference. Returns
#N/A error if cell
doesnt contain
ChemDraw molecule.
CHEM.NUM.
HBACCEPTORS
Returns number of
hydrogen bond
acceptors based on
topology. Returns
#N/A error if cell
doesnt contain
ChemDraw molecule.
ChemDraw 8
ChemDraw/Excel
Using ChemDraw/Excel Functions
209
ChemDraw
Administrator
Function
Action
Function
Action
CHEM.NUM.
HBDONORS
Returns number of
hydrogen bond donors
based on topology.
Returns #N/A error if
cell doesnt contain a
molecule.
CHEM.NUM.ATOMS
CHEM.SMILES
CHEM.COMPOSITION
Returns elemental
percent by weight for
all elements in
molecule unless
optional second
argument specifies a
single element symbol
as a string. In this case
the elemental percent is
expressed as a decimal
number between 0 and
1. (75.1% would be
0.751) Returns #N/A
error if the cell
referenced in first
argument doesnt
contain a ChemDraw
molecule, or if second
argument is not a valid
element symbol.
210
ChemDraw/Excel
ChemProp Properties
In ChemDraw/Excel, you can use the ChemProp Pro
functions to calculate the following properties:
Property
Function
LogP
CHEMPROP.LOGP
Molar Refractivity
CHEMPROP.MR
CambridgeSoft
Using ChemDraw/Excel Functions
Henrys Law
Constant
CHEMPROP.HENRY.
LAW.CONSTANT
Boiling Point
CHEMPROP.BOILING
Freezing
Temperature
CHEMPROP.FREEZING
ChemDraw
Property
CHEMPROP.CRITICAL.
PRESSURE
CHEMPROP.CRITICAL.
VOLUME
Heat of Formation
CHEMPROP.HOF
CHEMPROP.GIBBS
CHEMPROP.IDEAL.GAS
Inserting Functions
To insert a ChemDraw/Excel function into your
worksheet:
1. Select an empty cell.
ChemDraw 8
ChemDraw/Excel
Using ChemDraw/Excel Functions
211
Administrator
212
ChemDraw/Excel
CambridgeSoft
Using ChemDraw/Excel Functions
CAMEO
CAMEO (Computer-Assisted Mechanistic
Evaluation of Organic Reactions) is a modular
expert system. The application predicts the products
of organic reactions given starting materials,
reagents, and conditions. The analyses primarily
feature mechanistic reasoning and have been
extended to cover most of the major classes of
organic reactions (currently: Basic/Nucleophilic,
Acidic/Electrophilic, Electrophilic Aromatic
Substitution (EAS), Radical, Heterocyclic,
Pericyclic, Oxidative/Reductive, Carbene, Pd
Organometallic and Photochemical). An important
aspect of the application has been to clearly define
the logic behind the accurate prediction of products
and to simultaneously search for organizing
principles governing organic reactivity.
CAMEO was originally developed at Yale
University on a VAX machine as a standalone
application. It now has versions compatible with
Macintosh, Sun-Solaris, Linux and SGI/IRIX
CambridgeSofts version of CAMEO is an optional
plug-in for ChemDraw and ChemDraw/Excel. After
installation, a new menu will be included in both the
ChemDraw and ChemDraw/Excel toolbars.
CAMEO/Excel will allow the user to insert a
molecule into ChemDraw or ChemDraw/Excel,
choose reagents and conditions, and with one click
of the mouse, be presented with the products of the
reaction, their structure, and detailed information
about the reaction.
In this Chapter
Install CAMEO/Excel to be used in conjunction
with ChemDraw and ChemDraw/Excel. For
more information, see Installationbelow.
Configuring ChemDraw and ChemDraw/Excel
to use CAMEO/Excel. For more information,
see Configuring and Starting CAMEO/Excel
on page 214.
Submit a reaction using CAMEO/Excel to
predict the results. For more information, see
Submitting a Reaction on page 215.
Create a script, to be used with CAMEO/Excel,
to allow reaction settings to be saved and used
repeatedly with different starting materials. For
more information, see Creating a Script on
page 218.
Modify the settings of a previously generated
script job. For more information, see Editing a
Script on page 220.
Run a script from ChemDraw or
ChemDraw/Excel and view reaction results.
For more information, see Running a Script
on page 221.
Installation
CambridgeSoft has ported CAMEO into Windows
(from its Fortran roots) as an extension of
ChemDraw and ChemDraw/Excel. CAMEO/Excel
uses ChemDraw to retrieve structure information
regarding starting materials.
To install CAMEO/Excel, run the setup program
provided on the CAMEO/Excel CD.
ChemDraw 8
CAMEO
Installation
213
ChemDraw
Overview
Minimum System
Requirements
Administrator
Software Requirements
ChemDraw 8.0 Ultra
ChemOffice 8.0 Ultra (for use with
ChemDraw/Excel)
Microsoft Office 2000 or XP.
Configuring and
Starting CAMEO/Excel
Since CAMEO/Excel is meant to be used in
conjunction with another application, it should be
accessed from either ChemDraw or Excel.
After installing CAMEO/Excel, do the following to
start working:
From Excel
After installing CAMEO/Excel, there are a couple
additional steps that you must take before you can
use it with ChemDraw/Excel.
1. Start Microsoft Excel.
2. If ChemOffice and/or CSCAMEO menus are
From ChemDraw
1. Start ChemDraw.
2. Draw the starting material in a new or existing
ChemDraw document.
3. Use the selection tool (in the ChemDraw
214
CAMEO
CambridgeSoft
Configuring and Starting CAMEO/Excel
Transition Organometallic
Photochemical
Reaction Parameters
The Reaction Parameters section of the Submit
Reaction dialog box defines the conditions used to
predict the products in a given reaction. This section
has five parts:
Reaction Condition
Reagent
Solvent Information
Output Options
Special Conditions
Reaction Condition
CAMEO/Excel assigns default values for the
Reaction Conditions when you select a reaction type
in the Reaction Module.
Reaction Module
In CAMEO/Excel you can choose between 10
different reaction types. These are listed in the
Reaction Module pull-down menu of the Submit
Reaction dialog box. They include:
Carbene
Radical
Basic/Nucleophilic
Heterocyclic
Acidic/Electrophilic
Oxidation/Reduction
Electrophilic Aromatic Substitution
ChemDraw 8
CAMEO
Submitting a Reaction
215
ChemDraw
Submitting a Reaction
Pericyclic
Temperature Range
Administrator
Stoichiometry
Use the pull-down menu to choose a description of
the relative amount of reagent compared to the
amount of starting material.
Solvent Information
Use the solvent information section to choose a
solvent and the amount of dilution.
Reagent
Use the reagent section to choose a reagent for the
reaction. The options listed in the pull-down menu
depend on the reaction module chosen. In other
words, an option available in this menu when the
Carbene reaction module is chosen is Potassium
Hydroxide. If the reaction module is changed to
Radical, Potassium Hydroxide is no longer an
option. (To see what reagents would be options, see
Hetero, Pericycle Reaction Reagents on page 45.)
Solvent Dilution
A pull-down menu lists solvent dilution options as
follows:
Dilution Low
Dilution Average
Dilution High
Gas Phase
Protic Solvent
Selecting this checkbox makes water the default
solvent. Leaving the checkbox unchecked makes
DMSO the default solvent.
216
CAMEO
CambridgeSoft
Submitting a Reaction
Additional Solvent
Output Options
Use the Output Options section to save a MDL RXN
file. To choose this option, select the checkbox next
to Write RXN file and specify a filename in the
textbox next to Filename.
Special Condition
Selecting certain reaction modules displays a
section entitled Special Condition at the bottom of
the Submit Reaction dialog box. Presently those
modules are Carbene, Radical, and Photochemical.
Carbene Special Conditions
Reporting Options
Three checkboxes at the bottom of the Submit
Reaction dialog box control reporting options:
Report Delta Hf - if checked, the standard delta
Hf is reported for the starting material, product,
and reaction
Report Product Major/Minor Info - if checked,
it will be reported if the product is major of
minor, assuming the information is available
Report Bond Dissociation Energy - (only
available in ChemDraw) if checked, the bond
dissociation energy will be reported with bonds
connected to Hydrogen in black, and bonds not
connected to Hydrogen in red
1. Start ChemDraw.
ChemDraw 8
CAMEO
Submitting a Reaction
217
ChemDraw
menu.
5. Choose Acidic/Electrophilic for the Reaction
Administrator
Submit Reaction.
Creating a Script
A script is a file that saves all reaction parameters.
This may be desirable if, for example, the same
reaction is to be run with a number of different
starting materials.
A script saved in ChemDraw can be run from within
ChemDraw or Excel. The same is true for a script
created in Excel.
To create a script:
1. Start ChemDraw or Excel.
2. Insert a starting material.
3. Select Create CSCAMEO Script from the
CSCAMEO menu.
218
CAMEO
CambridgeSoft
Creating a Script
ChemDraw 8
CAMEO
Creating a Script
219
Administrator
3. Click Open.
Editing a Script
The Edit CSCAMEO Script menu command
allows you to modify the parameters in a previously
created script.
CSCAMEO menu.
A file dialog box appears.
220
CAMEO
Exit
If there is more then one reaction listed in the script
file, only one reaction can be edited at once. That is,
any changes made while the Reaction 2 parameters
are displayed, affect only Reaction 2.
CambridgeSoft
Editing a Script
Exit
Running a Script
1. Start ChemDraw or Excel.
2. Select a starting material.
Next
If there is more than one reaction in the script file,
clicking the Next button will display the next
reaction listed.
CSCAMEO menu.
The Run Cameo Script dialog box appears.
ChemDraw 8
CAMEO
Running a Script
221
ChemDraw
Save Reaction
Administrator
222
CAMEO
CambridgeSoft
Running a Script
Appendices
This section contains the Appendices for each of the
sections, arranged in the following order:
Section I: ChemDraw
Appendix A: The Chemistry of ChemDraw
Describes how ChemDraw interprets what
you draw and how you can help ChemDraw
better interpret what you mean.
Appendix B: How ChemProp/Draw Works
Describes how ChemProp/Draw enables you
to calculate predicted values of selected
physical and thermodynamic properties.
ChemDraw 8
A-1
Appendix
Administrator
A-2
CambridgeSoft
Chemical Intelligence in
ChemDraw
ChemDraw was designed as a tool to aid in chemical
communication. Most chemists would understand
AcOo-C6H4COOH immediately, whether or not
they recognized it as aspirin. Most computer
programs, however, require what is known as a
complete connection table, in this case, a
collection of 21 atoms connected by 5 double bonds
and 16 single bonds in a specific pattern. ChemDraw
takes what makes sense to a chemist and converts it
into what makes sense to another application.
This chemical intelligence can be used as a
sophisticated spelling checker for chemical
compounds. For example, if youre investigating
organic acids, a compound with the structural
formula CH3COO would probably represent acetic
Database Conventions
Most databases require not only that you draw a
structure in a way that makes sense, but that you
draw it in the way that the database expects it.
Consider ferrocene, which is represented in at least
four different ways in major databases:
Fe
Fe
Fe
Fe
Merck Index
ChemDraw 8
A-3
Database Conventions
Appendix
CH
HC
HC
Administrator
Fe
CH
CH
CH
Fe
CH
CH
Aldrich
CH
CH
MDL ACD
Triple bond.
Quadruple Bond.
A single bond near a closed circle is recognized as
aromatic:
Chemical Conventions
The following table describes the chemical
conventions understood by ChemDraw.
Bond
Description
Single bond, unspecified
stereochemistry.
Single bond, down
stereochemistry (into the plane of
the paper, away from the viewer),
from the first drawn atom to the
second drawn atom.
Single bond, up stereochemistry
(out of the plane of the paper,
toward the viewer), from the first
drawn atom to the second drawn
atom.
Single bond, mixture of up and
down stereochemistries in some
unspecified proportion.
Dative bond. Often used to indicate
polar bonds, such as the N-O bond
in pyridine N-oxide.
Double bond, with cis/trans
stereochemistry as drawn.
A-4
Atom Labels
A simple atom label may contain any of the
following:
Cl
A single element.
CH3
Me
A nickname.
H
N
Ala
C(OCH3)3
O(CH 2)4CH3
CH2 COOC (OPh)3 A series of any
combination of the
above.
CambridgeSoft
Chemical Conventions
CH2CCH3
(CH2)4
CH2 (CH2 )2CH 2
COO- Na+
COO-.Na+
COO-Na+
COO- . Na+
(COO-)3 . 3Na+
(COO-)3 . Na+ Na+ Na+
An unsuperscripted,
unsubscripted integer at
the start of a fragment is
recognized as a
stoichiometric multiplier
and is treated as if the
appropriate number of
fragments were drawn
explicitly.
H3CCH2C
(C H2)4 OH
COO-Na
ChemDraw 8
A-5
Chemical Conventions
Appendix
Administrator
H 2O
Charges
Charges may be created as part of a textual atom
label or with the appropriate symbol from the
Chemical Symbols Palette. Charges are always
assigned to a specific element in the atom label,
whose acceptable valences become those of the
similar isoelectronic neutral element.
O-
+NH3
NH3 +
(N+)H3
CO2-
CO(O-)
NH3 +
Fe++
Fe
2+
Fe
+2
NH3
(N+)H3
(N+)H3
A-6
CambridgeSoft
Chemical Conventions
Cl
CH2 13COOH
O
T
OD
Radicals
Radicals are indicated with the appropriate symbol
from the Chemical Symbols Palette. As with
charges, they are assigned to the nearest atom.
Radicals always occupy one free valence, in
addition to any charge effects.
Complexes
Compounds with electron pairs can act as Lewis
bases, bonding with Lewis acids that are electrondeficient. Similar behavior can be seen between lone
pairs and metals.
The best representation of these types of interaction
is with a dative bond from the electron-pair donor to
the acceptor. With a plain bond instead of the dative
bond, ChemDraw would report a valence error. The
dative bond more accurately represents the electron
donation.
Complexes may also be represented with explicit
lone pairs and without any bonds.
If you use a plain bond to indicate a complex, you
may want to set Abnormal Valence to Allowed in the
Atom Properties dialog.
F3B
Ph
Ph
NH3
Ph
HO
H-Dot/H-Dash
H-Dot and H-Dash symbols from the Chemical
Symbols Palette indicate the stereochemistry of a
single hydrogen atom. These symbols are most
commonly used in fused systems.
B
F
F
F
ChemDraw 8
A-7
Chemical Conventions
Appendix
D 3C
A superscripted number
before the element
symbol indicates isotope
numbers.
Heme, a compound
with two formal
covalent bonds and
two formal donoracceptor pairs.
Administrator
Fe
Cl
Cl
Ti
N
O
HO
Another
representation of
heme.
N
Fe
CO
OC
CO
Mn
N
O
HO
Multi-center Attachments
Multi-center attachments are meaningful only when
created using Add Multi-Center Attachment from
the Structure Menu. This command creates a
pseudo-atom that is disregarded during chemical
calculations, but still allows you to create diagrams
that look meaningful to an experienced chemist.
M
3 or -Allyl complex
Fe
-C5H5Mn(CO)3
Stereochemistry
Absolute stereochemistry is calculated for
tetrahedral atoms and double bonds according to the
Cahn-Ingold-Prelog (CIP) priority rules. The CIP
rules are designed to order ligands by their priority
and determine a descriptor based on the orientation
of the ordered ligands in space.
A ligand is an entity attached to a stereocenter. For
example, a tetrahedral carbon has four ligands
corresponding to its four substituents. When a
tetrahedral carbon is in a ring, it still has four
ligands: the two ligands outside the ring, a third
consisting of the ring unpeeled clockwise, and a
fourth consisting of the ring unpeeled
counterclockwise.
Five rules are used to determine the priority of
ligands are summarized below in simplified form.
For more detailed information, see the references.
They are checked sequentially as follows:
Rule 1Higher atomic number precedes lower
Rule 2Higher atomic mass precedes lower
A-8
CambridgeSoft
Chemical Conventions
Rule 5R precedes S
Abs
COOH
NH2
Stereochemical Indicators
After the ligands are ranked, an indicator is assigned
as shown in the following table.1
Stereocenter
Indicator
Double bond
COOH
NH2
Rel
COOH
NH2
COOH
COOH
OR
NH2
NH2
Rac
COOH
NH2
Stereochemical Flags
While the chirality of a specific stereocenter can be
indicated with the appropriate wedged, hashed, or
plain bond, sometimes it is useful to indicate the
relative stereochemistry of a molecule as a whole,
considering the relationship between all
stereocenters. Stereochemical flags apply to the
COOH
NH2
COOH
AND
The Racemic
flag indicates a
mixture of the
exact
stereoisomer as
drawn and its
enantiomer.
NH2
ChemDraw 8
A-9
Chemical Conventions
Appendix
The Relative
flag indicates
the exact
stereoisomer as
drawn, or its
enantiomer.
Polymer Representations
Administrator
References
Graphic Representations (Chemical Formulae) of
Macromolecules (Recommendations 1994) Pure
Appl. Chem., 66, 2469-2482 (1994).
Message
Description
An atom in this
label has an
invalid valence.
Query Properties
By their nature, query properties do not represent
actual chemical features, but describe broad classes
or groups of features. For information on using
query properties, see Chapter 9: Drawing Query
Structures.
Analysis Messages
When ChemDraw is unable to analyze your
structure fully, two general types of messages are
displayed:
A-10
CambridgeSoft
Chemical Conventions
Message
Description
Text not in
Formula style
wont be
interpreted.
This named
alternative group
contains no
attachment point.
Description
This named
alternative group
contains
fragments with
inconsistent
valences.
This named
Displayed for any Alternative
alternative group Group Box that is empty. This
contains no
is a status message only.
fragment.
Part of a molecule
is outside of the
alternative group
definition.
This isolated
bond is probably
not intended to
have chemical
significance.
ChemDraw 8
A-11
Chemical Conventions
Appendix
Formula cannot
be computed for
queries.
Message
Administrator
Message
Description
Message
Description
The stereocenter
has no
stereobonds
specified.
There is a valence
and charge error
somewhere in this
aromatic system.
The stereocenter
has conflicting or
ambiguous
stereobonds
specified.
A-12
CambridgeSoft
Chemical Conventions
Appendix B:
Pro How ChemProp/Draw Works
ChemProp/Draw Values
ChemProp/Draw enables you to calculate predicted
values of selected physical and thermodynamic
properties for structures of up to 100 atoms. The
following topics describe how ChemProp/Draw
obtains its values.
LogP
Henrys Law
Henrys Law ConstantThe air to water partition
coefficient that is expressed as ratio of vapor
pressure to water solubility or as a unitless
distribution coefficient that can be evaluated as a
ratio of the concentration in air to the concentration
in water.
Two methods are used to predict Henrys Law
constant.
1. The first is an approach based on the bond
ChemDraw 8
A-13
LogP
Appendix
Administrator
Molar Refractivity
A-14
Other Properties
Heat of Formation, Gibbs Free Energy, Ideal Gas
Thermal Capacity, Freezing Point, Critical
Temperature, Critical Pressure, and Critical
Volume are estimated using Jobacks fragmentation
method.
Normal Boiling Point and Melting Point
Estimated in K using two methods.
1. Joback's fragmentation method.
2. The Joback method as modified by Stein. All
CambridgeSoft
Molar Refractivity
Appendix C:
UltraHow ChemNMR Pro Works
Overview
ChemNMR Pro estimates chemical shifts for all
hydrogen or carbon atoms for which additivity rules
are available. Following a hierarchical list, it first
identifies key substructures of a molecule. A
substructure provides the base value for the
estimated shift. For example, benzene would be
identified as the key substructure of trinitrotoluene.
ChemNMR Limitations
The program handles the following elements:
H, D, He, Li, Be, B, C, N, O, F, Ne, Na, Mg, Al, Si,
P, S, Cl, Ar, K, Ca, Sc, Ti, V, Cr, Mn, Fe, Co, Ni, Cu,
Zn, Ga, Ge, As, Se, Br, Kr, Rb, Sr, Y, Zr, Nb, Mo, Tc,
Ru, Rh, Pd, Ag, Cd, In, Sn, Sb, Te, I, Xe, Cs, Ba, La,
Ce, Pr, Nd, Pm, Sm, Eu, Gd, Tb, Dy, Ho, Er, Tm, Yb,
Lu, Hf, Ta, W, Re, Os, Ir, Pt, Au, Hg, Tl, Pb, Bi, Po,
At, Rn, Fr, Ra, Ac, Th, Pa, U, Nep, Pu, Am, Cm, Bk,
Cf, Es, Fm, Md, No, Lr. Functional groups are
expanded automatically.
In case of 1H NMR, it estimates shifts of about 90%
of all CHx-groups with a standard deviation of
0.2 0.3 ppm. The use of polar solvents may
strongly increase these deviations. It does not
estimate shifts of hydrogen atoms bonded to
heteroatoms because they are significantly affected
by solvents, concentration, impurities, and steric
effects.
In case of 13C NMR, it estimates over 95% of the
shifts with a mean deviation of -0.29 ppm and
standard deviation of 2.8 ppm.
For more information see:
Frst, A.; Pretsch, E. Anal. Chim. Acta 1990, 229,
17.
ChemDraw 8
A-15
ChemNMR Limitations
Appendix
Administrator
A-16
CambridgeSoft
ChemNMR Limitations
Appendix D: Automation
Macintosh
Windows
ChemDraw 8
A-17
Macintosh
Appendix
Administrator
A-18
CambridgeSoft
Windows
file format.
b. Type a name for the document.
Appendix
ChemDraw 8
A-19
ACS 1996
Bold Width: 2 pt
HO
O
Hash Spacing: 2.5 pt
H
H
HO
Morphine
Morphine
A-20
CambridgeSoft
Drawing, Atom Label, and Caption Text Settings in Journal Style Sheets or Stationery Pads
Adv. Synth. Catal.
Fixed Length: 17 pt
Bold Width: 2 pt
HO
Line Width: 1 pt
Margin Width: 1.6 pt
O
N
H
HO
Morphine
Morphine
Caption Size: 12 pt
Drawing Area (Width x Height): 540 pt x 720 pt
Page Size: US Letter
Reduction (%): 100
ChemDraw 8
A-21
Appendix
Drawing, Atom Label, and Caption Text Settings in Journal Style Sheets or Stationery Pads
Helvetica Chimica Acta
Administrator
Fixed Length: 17 pt
Bold Width: 2.9 pt
HO
Hash Spacing: 2 pt
Morphine
Morphine
A-22
CambridgeSoft
Drawing, Atom Label, and Caption Text Settings in Journal Style Sheets or Stationery Pads
Fixed Length: 18 pt
Bold Width: 2.5 pt
HO
Line Width: 1 pt
Margin Width: 2 pt
O
N
H
HO
Morphine
Morphine
Appendix
ChemDraw 8
A-23
Drawing, Atom Label, and Caption Text Settings in Journal Style Sheets or Stationery Pads
Fixed Length: 14.4 pt
Administrator
J. Mol. Mod.
Bold Width: 2 pt
Line Width: 0.6 pt
HO
O
H
HO
Morphine
A-24
CambridgeSoft
Drawing, Atom Label, and Caption Text Settings in Journal Style Sheets or Stationery Pads
Fixed Length: 30 pt
New Document
Bold Width: 2 pt
Line Width: 1 pt
HO
Margin Width: 2 pt
Hash Spacing: 2.7 pt
Chain Angle (degrees): 120
H
Atom Label Size: 10 pt
Caption Font (Win/Mac): Times New Roman/Times
Caption Size: 12 pt
Morphine
ChemDraw 8
A-25
Appendix
HO
Drawing, Atom Label, and Caption Text Settings in Journal Style Sheets or Stationery Pads
Administrator
New Slide
Fixed Length: 30 pt
Bold Width: 4 pt
HO
N
H
HO
Morphine
A-26
CambridgeSoft
Drawing, Atom Label, and Caption Text Settings in Journal Style Sheets or Stationery Pads
Fixed Length: 20 pt
Phytomedicine
Appendix
HO
Morphine
Caption Size: 12 pt
Drawing Area (Width x Height): 540 pt x 720 pt
Page Size: US Letter
Reduction (%): 100
ChemDraw 8
A-27
Drawing, Atom Label, and Caption Text Settings in Journal Style Sheets or Stationery Pads
Administrator
HO
Line Width: 0.016 cm
Margin Width: 0.044 cm
O
H
H
HO
Morphine
A-28
CambridgeSoft
Drawing, Atom Label, and Caption Text Settings in Journal Style Sheets or Stationery Pads
SYNTHESIS, SYNLETT
Fixed Length: 17 pt
Bold Width: 2 pt
Line Width: 0.8 pt
HO
H
H
HO
Morphine
Appendix
ChemDraw 8
A-29
Administrator
A-30
CambridgeSoft
Line 2
77
Line 3
0.0000
0.5000
0.0000
Line 4
-0.8667
0.0000
0.0000
Line 5
-0.8667
-1.0000
0.0000
Line 6
0.0000
-1.5000
0.0000
Line 7
0.8667
-1.0000
0.0000
Line 8
0.8667
0.0000
0.0000
Line 9
0.0000
1.5000
0.0000
Line 10
1211
Line 11
2311
Line 12
3411
Line 13
4511
Line 14
5611
Line 15
1611
Line 16
6711
OH
1
2
3
ChemDraw 8
A-31
Appendix
Line 1
Administrator
value
bond type
Hashed.
Bold.
Wavy.
10
11
12
13
14
15
16
Double/Aromatic (bond
property).
bond type
Single.
Dashed.
A-32
CambridgeSoft
value
bond type
value
bond type/position
17
Single/Aromatic (bond
property).
16
32
A crossed bond.
64
bond type/position
ChemDraw 8
A-33
Appendix
Administrator
A-34
CambridgeSoft
conflicts.
2. Check the system requirements for the software
Appendix
Serial Numbers
When contacting Technical Support, you must
always provide your serial number. This serial
number was on the outside of the original
ChemDraw box, and is the number that you entered
when you launched ChemDraw for the first time. If
you have thrown away your box and lost your
installation instructions, you can find the serial
number in the following ways:
Macintosh
With ChemDraw launched, choose About CS
ChemDraw from the Apple menu. The serial
number appears at the bottom left.
Windows
With ChemDraw launched, choose About CS
ChemDraw from the Help menu. The serial number
appears at the bottom left.
ChemDraw 8
A-35
Serial Numbers
Administrator
http//www.cambridgesoft.com/support/
codes.cfm
Troubleshooting
This section describes steps you can take that affect
the overall performance of ChemDraw, as well as
steps to follow if your computer crashes when using
a CS software product.
Launching
If ChemDraw cant find the ChemDraw Items
folder, you are not able to launch the program. For
additional information about the appropriate
location, see The ChemDraw Items Folder on
page 18.
Performance
Below are some ways you can optimize the
performance of ChemDraw:
Macintosh: Increase the total amount of
memory that the application can use:
Select the ChemDraw application icon in the
Finder when ChemDraw is not running.
From the Edit menu, choose Get Info.
Increase the memory allocation in the
Preferred size text box in the Memory
Requirements section of the dialog box.
Windows: In the Performance tab in the
System control panel (Windows NT 4.0),
allocate more processor time to ChemDraw.
Install more physical RAM. The more you
have, the less ChemDraw will have to access
your hard disk to use Virtual Memory.
Increase the Virtual Memory (VM). Virtual
memory extends RAM by allowing space on
your hard disk to be used as RAM. However,
A-36
System Crashes
ChemDraw should never crash, but below are the
steps you should go through to try to resolve issues
that cause computer crashes while using a CS
software product.
1. Restart your computer (Macintosh) or restart
CambridgeSoft
Troubleshooting
at:
http://www.cambridgesoft.com/support/mail
Appendix
ChemDraw 8
A-37
Troubleshooting
Administrator
A-38
CambridgeSoft
Troubleshooting
ID
Reagent Name
Potassium Hydroxide
KOH
45
Triethyl Amine
n_Butyllithium(n-BuLi)
46
Thiophenol(PhSH)
90
N/A
47
Tributylgermanium
Hydride/AIBN
91
Acetic Anhydride
Triphenyl phosphine
(PPh3)
48
N_Chlorosuccinimide
(NCS)
92
Acetone
Sodium Ethoxide
(EtONa)
49
Bromotrichloro methane
(BrCCl3)
93
Acetonitrile
50
Dibenzoyl peroxide
(Bz2O2)
94
Benzene
Sodium Borohydride
(NaBH4)
95
t_Butanol
Ammonia (NH3)
52
HexabutylDitin
(Bu3SnSnBu3)
96
Carbon DiSulfide
Sodium Methoxide
(MeONa)
53
97
Carbon Tetrachloride
10
98
Chloroform
ChemDraw 8
ID
Reagent Name
Appendix
ID
A-39
Administrator
ID
Reagent Name
ID
Reagent Name
ID
Reagent Name
11
55
Azobisisobutyro Nitrile
(AIBN)
99
Cyclohexane
12
Potassium Butoxide
(BuOK)
56
Disiamyl
Borane_Sia2BH
(Sia2BH)
100
DiethylEther
13
Sodium Acetate
(AcONa)
57
Aluminum Hydride
(AlH3)
101
Diglyme
14
58
H2/Pd
102
Dimethyl Formamide
15
Sodium Thiophenoxide
(PhSNa)
59
Ti(III)
103
dimethyl Sulfoxide
16
Lithium
60
Diisopropylamide (LDA)
NaBH4
104
p_Dioxane
17
Raney Ni
105
Ethanol
18
Potassium Carbonate
(K2CO3)
62
Zn/H+
106
EthylAcetate
19
Acetic Acid(HOAc)
63
LiAlH4
107
Glyme
20
NaNH3
108
HMPT_HMPA_DMPU
21
Fluorine (F2)
65
N2H2/KOH/HEAT
109
Methanol
22
Mercuric Acetate
(HgOAc)
66
Borane (BH3/B2H6)
110
MethylEthyl Ketone
23
Toluenesulfonic Acid
67
Al/Hg2
111
Methylene chloride
24
9-BBN
112
N_MethylPyrrolidinone
A-40
CambridgeSoft
Reagent Name
ID
Reagent Name
ID
Reagent Name
25
Chlorine (Cl2)
69
DIBAL
113
Morpholine
26
Aluminum Trichloride
(AlCl3)
70
KMnO4/RT
114
Petroleum Ether
27
71
SeO2
115
Pipiridine
28
72
Quinoline
116
i_Propanol
29
Bromine (Br2)
73
KMnO4/HEAT
117
Pyridine
30
74
MnO2
118
Sulfolane
31
Phosphoric Acid
(H3PO4)
75
O2
119
Tetrahydrofuran
32
Water
76
OsO4
120
Toluene
33
Iodine (I2)
77
CrO3/H+
121
Triethylamine
34
Iron Trichloride(FeCl3)
78
I2
122
TriethylOrthoformate
35
Sulfuric Acid
79
RCO3H
123
Trifluoroacetic Acid
36
P2S5
80
CrO3/Py
124
Water
37
P 2 O5
81
Pd/C
125
Xylene
38
82
H2O2/NaOH
126
Hydrazine N2H4
39
Tributyltin
Hydride/AIBN
83
HIO4
127
Pd(PPH3)4
40
Bromine(Br2)/UV
84
L-(+)-(R,R)diethyltartrate
128
PdCl2
ChemDraw 8
Appendix
ID
A-41
Administrator
ID
Reagent Name
ID
Reagent Name
ID
Reagent Name
41
Chloroform CHCl3
85
D-(-)-(S,S)diethyltartrate
129
PdCl2(PPh3)2
42
t_Butyl
Hypochlorite(tBuOCl)
86
Zinc Chloride
130
Pd(PPh2CH2CH2PPh2)2
43
Diphenyl
TinDihydride/AIBN
87
Tetra chloride
131
PalladiumDiacetate
44
N_Bromosuccinimide
(NBS)
88
Titanium Tetrachloride
132
(dba)3Pd2
Solvents
ID
Solvent Name
ID
Solvent Name
ID
Solvent Name
Acetic Acid
13
Dimethyl Formamide
25
Petroleum Ether
Acetic Anhydride
14
Dimethyl sulfoxide
26
Pipiridine
Acetone
15
p-Dioxane
27
i-Propanol
Acetonitrile
16
Ethanol
28
Pyridine
Benzene
17
Ethyl Acetate
29
Sulfolane
t-Butanol
18
Glyme
30
Tetrahydrofuran
Carbon Disulfide
19
HMPT(HMPA)/DMPU
31
Toluene
Carbon Tetrachloride
20
Methanol
32
Triethylamine
Chloroform
21
33
Triethyl Orthoformate
10
Cyclohexane
22
Methylene Chloride
34
Trifluoroacetic Acid
A-42
Solvents
CambridgeSoft
ID
Solvent Name
ID
Solvent Name
ID
Solvent Name
11
Diethyl Ether
23
N-Methyl-Pyrrolidinone 35
Water
12
Diglyme
24
Morpholine
36
Xylene
ID
Reagent Name
ID
Reagent Name
Potassium Hydroxide
KOH
Ammonia
15
Sodium Thiphenoxide
(PhSNa)
n_Butyllithium(n-BuLi)
Sodium Methoxide
(MeONa)
16
Lithium
Diisopropylamide (LDA)
10
Triphenyl phosphine
(PPh3)
11
Sodium Iodine
18
Potassium Carbonate
(K2CO3)
Sodium Ethoxide
(EtONa)
12
Potassium Butoxide
(BuOK)
19
Triethyl Amine
13
Sodium Bromide(NaBr) 14
Appendix
ID
Reagent Name
ID
Reagent Name
ID
Reagent Name
Tributyltin
Hydride/AIBN
Carbon Tetrachloride
CCl4
13
Sodium Borohydride
(NaBH4)
ChemDraw 8
A-43
Administrator
ID
Reagent Name
ID
Reagent Name
ID
Reagent Name
Bromine (Br2)/UV
Thiophenol (PhSH)
14
HexabutylDitin
(Bu3SnSnBu3)
Chloroform CCl3
Tributylgermanium
Hydride/AIBN
15
t_Butyl Hypochlorite
(tBuOCl)
10
N_Chlorosuccinimide
(NCS)
16
Di_t_Butyl Peroxide
((tBu)2O2)
Diphenyl
TinDihydride/AIBN
11
Bromotrichloro methane 17
(BrCCl3)
N_Bromosuccinimide
(NBS)
12
Dibenzoyl peroxide
(Bz2O2)
Azobisisobutyro Nitrile
(AIBN)
Reagent Name
ID
Reagent Name
ID
Reagent Name
Nitric Acid
17
Sulfuric Acid
18
P2S5
Fluorine (F2)
11
Bromine (Br2)
19
P2O5
Mercuric Acetate
(HgOAc)
12
20
Silver Nitrate
Toluenesulfonic Acid
13
Phosphoric Acid
21
Zinc Chloride
Hydrobromic Acid
(HBr)
14
Water
22
Tetra Chloride
Chlorine (Cl2)
15
Iodine
23
Titanium Tetrachloride
A-44
CambridgeSoft
ID
Reagent Name
ID
Reagent Name
Aluminum Trichloride
(AlCl3)
16
ID
Reagent Name
ID
Reagent Name
ID
Reagent Name
Potassium Hydroxide
KOH
14
27
Nitric Acid
n_Butyllithium (n-BuLi) 15
Sodium Thiophenoxide
(PhSNa)
28
16
Lithium
29
Diisopropylamide (LDA)
Bromine (Br2)
Triphenyl phosphine
(PPh3)
17
SodiumAmide NaBH2
30
Sodium Ethoxide
(EtONa)
18
Potassium Carbonate
(K2CO3)
31
Phosphoric Acid
19
32
Water
Iodine
Ammonia (NH3)
21
Flourine(F2)
34
Sodium Methoxide
(MeONa)
22
Mercuric Acetate
(HgOAc)
35
Sulfuric Acid
10
Sodium Cyanide(NaCN) 23
Toluenesulfonic Acid
36
P2S5
11
P2O5
ChemDraw 8
24
A-45
Appendix
ID
Administrator
ID
Reagent Name
ID
Reagent Name
ID
Reagent Name
12
Potassium Butoxide
(BuOK)
25
Chlorine (Cl2)
38
13
Sodium Acetate
(AcONa)
26
Aluminum Trichloride
(AlCl3)
Reagent Name
ID
Reagent Name
ID
Reagent Name
Na2Cr2O7
17
PCC
32
DIBAL
Pb(OAc)4
18
NaIO4
33
LiNH3
KMnO4
19
MnO2
34
H2/RH
MCPBA
20
(COCl2)2
35
LiBH4
CrO3
21
PDC
36
AlH3
Hg(OAc)2
22
NaOCl
37
Zn/AcOH
SeO2
23
38
H2/Pd-on-C
H2 O2
24
39
NaBH3CN
CrO2Cl2
25
Swernoxidation
40
LiAlH(OMe3)
10
Cu(OAc)2
26
H2/Raney Ni
41
Zn/HCl
11
OsO4
27
NaBH4
42
Zn/Lindlar
12
CH3CO3H
28
Sia2BH
43
Borane
13
CrO3(pyr)2
29
Li/NH3/ROH
44
LiAlH4
A-46
CambridgeSoft
ID
Reagent Name
ID
Reagent Name
ID
Reagent Name
14
HIO4
30
H2/PtO2
45
Zn/Hg
15
RuO4
31
LiAlH(t-BuO)3
46
N2H4/KOH
16
OppenauerReagent
ID
Reagent Name
Hydrazine N2H4
Pd(PPh2CH2CH2PPh2)2
Pd(PPH3)4
PalladiumDiacetate
PdCl2
(dba)3Pd2
PdCl2(PPh3)2
ChemDraw 8
Appendix
ID
A-47
Administrator
A-48
CambridgeSoft
Index
Numerics
C, H shifts, estimating 135
35 mm Slide Boundary lines 166
3D models 131
3D Query Properties 145
13
A
Abnormal Valence 142
Abnormally shaped arrows, creating 93
Absolute flag, drawing 148
ACS Document 1996 A20
Actual Size command 167
ACX information, finding 194
Acyclic Chain Tool, description 7
Acyclic chains
adding 58
length 58
Add
3D query property 146
chemical names 72
column to template 124
row to template 124
to selection 99
Add Frame 89
Adding
structures in ChemDraw/Excel 204
Aligning objects
Align Submenu 170
overview 170
rulers 168
with crosshair 169
Aligning Structures 24
Alternative Groups
attachment point numbering 157
attachment point symbol 155
Attachment Rank indicators 155
defining 154
description 154
multiple attachment points 156
Always Display and Print Atom Mapping 158
ChemDraw 8
Analysis
information 128
messages A10
Analysis window 9
Anion, drawing 85
Anonymous Alternative Groups 157
Apple Events, description A17
Apply Settings command 13
Arc Tool
description 7
using 89
Arcs
drawing 89
resizing 89
arcs 89
Arrow Tool
description 7
overview 86
palette 86
Arrows
autoscaling 180
created with curves 93
resizing 87
Aspect Ratio, changing 105
Assigning
atom mapping 157
structures to spectra 134
Atom
moving 100
numbering 76
query properties 137
Atom Label text boxes, closing 65
Atom Labels
automatic justification 68
creating 72
deleting 73
editing 73
hotkeys 74
justification 68
layering 73
Index
Administrator
ii
Index
Autoscale, contd.
template color 121
when transferring 179
B
Background color, printing 19
Baseline style, captions 66
Benzene Ring
changing orientation 57
drawing 57
Benzene Ring Tool 55
Bezier curves 90
BitMap file format 184
Bitmapped
Fonts 79
printing quality 19
bmp files 184
Boiling Point
calculation A14
definition 132
Bold Bond Tool icon 52
Bold Wedge Bond Tool icon 52
Bold Width 50
Bond crossings
changing 60
white space 50
Bond order, changing 61
Bond Properties
defining 143
descriptors 143
reaction center 145
removing 143
topology 145
types 144
viewing 143
Bond query indicators 143
Bond Spacing, description 49
Bond tool
description 6
icons 52
repeating a label 76
Bonds
adding 114
autoscaling 179
changing bond type 59
CambridgeSoft
Bonds, contd.
changing type 58
double either 144
drawing 53
drawing by clicking 54
editing 58
Fixed Length 53
layering 60
margin width 50
multi center attachment 114
orientation, changing 59
orientation, dative bond 54
orientation, wedge bond 54
quadruple 53
selecting 98
types A4
Border of page 163
Boxes
drawing 87
rotating 88
Braces 88
Bracket
usage 152
Brackets
description 7
drawing 88
paired 89
setting properties 151
single 88
tool 88
using to represent polymers 151
Bring to Front command 171
Bruker JCAMP file format 187
C
Calculating
chemical properties 131
elemental analysis 129
exact mass 129
formula 129
Molecular Weight 129
CambridgeSoft web site, accessing 195
CambridgeSoft.com 195
ChemDraw 8
CAMEO
Creating scripts 218
Editing scripts 220
Extra Reagent Drop Down Menu A39
Getting Started 214
Hetero, Pericycle Reaction Reagent list A45
Installation 213
Overview 213
Oxidation Reduction Reaction Reagent list A46
Reaction module 215
Reporting options 217
Running scripts 221
Submitting a reaction 215
Can. J. Chem. Document A20
Caption text boxes
closing 65
creating new line 65
Captions
Analysis information 129
autoscaling 180
coloring 70
converting to structures 63
creating 70
creating tables 174
editing 71
formula 66
inserting from structure 72
inserting rows in tables 175
justification 67
setting Font, Size and Styles 69
subscript 66
superscript 66
Table column spacing 175
text overview 70
width 71
Carbon-13 shifts, see 13C, 1H shifts, estimating
Cation, drawing 85
CCITT Group 3 and 4 189
CD Template 184
cds format 185
cdx
file format 184
saving as 16
cdxml format 185
Center on Page command 170
Index
iii
Administrator
iv
Index
ChemDraw/Excel
adding structure files 204
adding structures 204
adding structures as SMILES 204
adding structures by name 205
adding structures with ChemDraw 204
aligning structures 208
exporting 203
Get ChemDraw List command 202
importing tables 201
naming molecules 207
overview 201
searching 205
starting 201
viewing structures 207
ChemFinder.com 193
Chemical name, structure from 62
Chemical properties
calculating 131
ChemProp/Draw 131
Chemical Properties window 10, 131
Chemical Symbols
palette 84
rotating 86
tool 7, 84
Chemical syntax checking 61
Chemical Warnings
overview 61
suppressing 21, 61
Chemically significant text A5
Chemicals, purchasing online 194
Chemistry
checking 127
of ChemDraw A3
ChemNews.Com 195
ChemNMR
using 135
ChemOffice SDK, accessing 197
ChemProp, using with ChemDraw/Excel 210
ChemProp/Draw
calculations A13
description A13
using 131
ChemStore.com 194
chm files 185
CambridgeSoft
CIP Rules A8
Clearing
mapping 159
spectrum-structure assignments 134
stereochemical markers 129
Click to select objects 98
Clipboard 177
Check Structure 128
copy 101
cutting 100
moving objects 100
pasting 100
Clipping files 179
CLogP 132
Closed Brackets, rotating 88
Closed style, shapes 92
Closing
caption text box 65
ChemDraw 20
documents 18
CMR 132
CMYK, Planar and Contiguous 186, 189
Color
autoscaling 180
menu 118
overview 117
saving settings 121
Color dialog box 119, 120
Color Palette 119
Coloring
captions 70
objects 118
Column spacing 175
Compression 189
Connection Table
example file A31
file format 185, A31
Contract label 112
Conventions 3
Convert name to structure, limitations 62
Convert structure to name, automatic captions 72
Converting
captions to structure 63
name to structure 62
to 3D 131
ChemDraw 8
Copy
and Check Structure 128
As SLN command 178
As SMILES command 177
duplicating objects 101
objects 101
with Clipboard 177
with drag and drop 178
Creating
atom labels 72
HotKeys 75
mirror images 103
new document 14
SLN strings 178
tables 174
templates 124
text 65
Critical Pressure
calculation A14
definition 132
Critical Temperature
calculation A14
definition 132
Critical Volume
calculation A14
definition 132
Crosshair
displaying 169
moving 169
using to align objects 169
CT file format 185
CTP file format 184
CTR file format 184
CTS file format 188
Curves
autoscaling 180
for creating arrows 93
segment, deleting 92
Custom templates 123
Customized settings, saving 13
Customizing
ChemDraw 12
menu extension DLLs A17
saving document settings 13
using Scripts 20
Index
Cut
Administrator
objects 100
Cycloalkane rings, converting to delocalized rings
56
Cyclohexane Chair Ring Tool
description 55
orientation 56
Cyclohexane Ring Tool 55
Cyclooctane Ring Tool 55
Cyclopentadiene Ring Tool 55
Cyclopentadiene Ring, changing orientation 57
Cyclopentadiene rings, drawing 57
Cyclopentane Ring Tool 55
Cyclopropane Ring Tool 55
D
Daggers 89
Dashed Bond Tool icon 52
Databases
support for query structures 137
supported 137
Dative Bond
drawing 54
Tool icon 52
Default
atom properties, resetting 138
bond properties, resetting 143
changing 13
document location 14
file format 15
save file format 17
Stationery pad 12
Style Sheet 12
Defined Nickname 110
Deflate compression 189
Delete Column, from template 125
Delete Row, from template 125
Deleting
atom labels 73
Backspace key 99
curve segment 92
Delete key 99
Nicknames 112
objects 99
Pen tool shapes 92
vi
Index
CambridgeSoft
Drawing, contd.
bonds by clicking 54
boxes 87
charge symbols 85
cyclopentadiene rings 57
double bonds 52
double either bonds 53
dz2- orbitals 84
fixed length bonds 53
free sites 148
H-Dash Symbol 84
H-Dot Symbol 84
mirror images 103
orbitals 82
quadruple bonds 53
radicals 85
resonance delocalized rings 56
rings 56
rings with fixed length 56
sigma orbitals 82
single bonds 52
s-orbitals 82
stereochemical symbols 148
structure automatically from name 62
triple bonds 53
with templates 122
Drawing area 163
Drawing daggers 89
Drawing Elements
autoscaling 180
color 87
distorting 88
fill patterns 87
resizing 88
rotating 88
Drawing Elements Tool 7
Drawing settings
changing defaults 13
Fixed Angles 54
margin width, effect on atom labels 73
margin width, effect on bond crossing 50
Duplicating
labels 76
objects 101
dx file format 187
ChemDraw 8
E
Editing
atom labels 73
atom numbers 77
bond orientation 59
bond type 58
bonds 58
captions 71
embedded objects 181
generic nickname file 149
query indicators 147
Element
list 149
not-list 150
recognized A7
Elemental Analysis
caption 129
description 129
Embedding objects 181
Encapsulated PostScript, see EPS file format
Enclosing objects 89
Enlarge
document window 163
page size 166
EPS file format
overview 185
Text 185
Eraser Tool 6
Eraser Tool, changing bond order with 61
Error checking 61
Error Messages A10
Exact Mass
caption 129
definition 128
Excel
Functions 208
Excel add-in, see ChemDraw/Excel 201
Excel Functions 208
Exiting 20
Expanding labels 113
Exporting
checking structure 128
compatibility 159
Index
vii
Administrator
Exporting, contd.
in ChemDraw/Excel 203
mapping 159
PNG 188
query properties 159
query structures 159
TIFF 189
using file formats 183
F
FAQs
online, accessing 196
Technical Support A35
File Format
Stationery pad 185
File format
Bitmap 184
cdx 16
cdxml 185
ChemDraw 184
ChemDraw 3.5 185
ChemDraw Stationery 185
Connection Table 185
connection table A31
CT 185
CTP 184
CTR 184
cts 188
EPS (TEXT) 185
GIF 186
ISIS 186
ISIS/Reactions 186
JDX 187
MDL MolFile 187
MDL RGFile 187
MSI MolFile 187
native 16
PICT 188
PICT scaled 4x 188
PNG 188
rxn 186
SMD 188
SPC 188
style sheet 185
Template 184
viii
Index
CambridgeSoft
G
G Groups 154
Galactic Industries file format 188
Generic Groups 154
Generic Nicknames
description 148
editing file 149
Get ChemDraw/Excel List 202
Getting Started Tutorial 21
Gibbs Free Energy
calculation A14
definition 132
GIF format 186
GRAMS software 188
Graphical User Interface 5
Grouping
orbitals 82
using 106
Grouping Objects 106
Groups
Integral 106
GUI, see Graphical User Interface
H
Hard Coded HotKeys 75
Hash Spacing, description 50
Hashed Bond Tool icon 52
Hashed Wedge Bond tool icon 52
H-Dash Symbol, drawing 84
H-Dot and H-Dash, specification A7
H-Dot Symbol, drawing 84
Headers, creating 164
Heat of Formation
calculation A14
definition 132
Help
Windows 3
Henrys Law, definition 132
Hide Crosshair command 170
Hide Rulers command 169
ChemDraw 8
Hiding
Atom Numbering 77
palettes 8
High resolution
non-PS printing 19
printing 19
Highlight box
selecting 98
size 55
Hollow Wedge Tool icon 52
Home page, CambridgeSoft 195
Hotkeys
Creating 75
File 75
Hard-coded 75
labeling by pointing 74
labeling multiple atoms 75
labeling the last atom drawn 74
labeling with a selection tool 74
overview 74
How to use this guide 3
Hydrogens, implicit 139
Hyphens, Font submenu 67
I
Ideal Gas Thermal Capacity, calculation A14
Implicit Hydrogens 139
Imported objects, selecting 98
Imported Picture 184
Importing
spectral data 187, 188
tables in ChemDraw/Excel 201
using file formats 183
Include ChemDraw LaserPrep 183
Indicators
Atom Numbering 77
query 147
query, editing 147
query, positioning 147
stereochemical
stereochemistry 130, A9
stereochemistry, positioning 130
Indicators, stereochemical 148
Info window 10
Insert Name as Structure 62
Index
ix
Administrator
Inserting
graphics 190
name as structure 62
objects 190
references in MS Word 181
rows in tables 175
Installing CAMEO/Excel 213
Integral Groups, Creating 106
Interface 5
Internet, CambridgeSoft web site 195
IR spectra, see spectra
ISIS
Reactions 186
SKC file format 186
TGF file format 186
Isotopes
specifications A7
Isotopes Table 142
isotopes text file 142
J
J. Mol. Mod.
(1 Column) A20
(2 Column) A20
JCAMP file format 187
JDX file format 187
Jobacks Fragmentation Method A14
Joining
structures 105
Joining Objects 105
Justification
atom labels 68
captions 67
K
Kekule structures 56
L
Lab supplies, purchasing online 194
Labels
contracting 112
expanding 113
Landscape page orientation 166
Lasso tool
selecting objects 97
toggling with Text Tool 76
Index
Layering
atom labels 73
objects 171
Layout, page 163
Lewis dot symbol, see Lone Pair Symbol
Ligand, defined A8
Limitations, name-to-structure 62
Line Width 50
Lines, drawing 88
Link nodes 150
List Nicknames command 112
LogP
calculation A13
Lone Pair Symbol 85
M
m/e, displaying 129
Magnifying
with Magnification control 168
with View menu 167
Make Spectrum-Structure Assignment 134
Manual Mapping
clearing 159
overview 158
Mapping
atom 157
automatic 158
clearing 159
exporting 159
manual 158
reaction 157
Margin Width
adjusting 50
description 50
effect on Bond crossings 50
specifying 73
Margin width, specifying 73
Marquee tool 97
Mass Fragmentation Tool 133
Mass spectra
importing as JDX 187
importing as SPC 188
mass/charge, displaying 129
Maximize objects 167
MDL MolFile 187
CambridgeSoft
N
Name
inserting as structure 62
of structure, inserting 72
ChemDraw 8
Name to structure
converting 62
limitations 62
paste special 63
with German names 62
Name, automatic structure from 62
Native file format 16
New Color Button 119
New Command 14
New document 14
New Slide A20
New Template, creating 123
Nicknames
defining 110
deleting 112
generic 148
overview 109
troubleshooting 111
nicknames.dat 109
NMR, see ChemNMR, Spectra
Non-PostScript printing
high resolution 19
Macintosh 183
Normal Boiling Point A14
Normal view 167
Numbering atoms 76
O
Object
Add Frame 89
Align 24
Distribute 171
Group 106
Join 105
Ungroup 106
Objects
aligning 169
centering 170
deleting 99
Distributing 171
distributing 171
grouping 106
joining 105
moving 99
ordering 171
Index
xi
Administrator
Objects, contd.
reflecting 103
selecting all 99
ungrouping 106
using crosshair with 169
using rulers with 168
OLE 181
OLE automation A17
Online Help, see Help
Online Menu
Browse ChemStore.com 194
CambridgeSoft Home Page 195
ChemOffice SDK 197
CS Chem3D Technical Support 196
Lookup Suppliers on ChemStore.com 193
Register online 196
Open command 15
Open Special command 14
Opening
ChemDraw/Excel 201
Orbital Tool
description 7
fill patterns 81
Fixed Angle 82
overview 81
Orbitals
drawing 82
grouping 82
type 81
Ordering objects 171
Orientation
Benzene Ring Tool 57
Cyclohexane Chairs 56
Cyclopentadiene Ring Tool 57
double Bond 59
of page 166
rings 56
templates 122
user-defined templates 124
Original view 167
Overlap, multipaged documents 164
P
Packbits, compression 189
xii
Index
Page
border 163
layout 163
orientation 166
overlap 164
setup 165
Page Definition Language
PostScript 19
QuickDraw 19
Page Setup
page layout 165
saving settings 166
Paged documents 163
Paired brackets 89
Palette
Arcs 89
Brackets 88
Chemical Symbols 84
color 119
Multiple bonds 52
orbital tools 81
Query tools 147
single bonds 52
Palettes
showing 8
tearing off 8
Paper Size 166
Parentheses 88
Paste
Duplicating objects 101
objects 100
Paste Special
name as structure 63
SMILES 178
Pen Tool 7
Pen tool shapes
deleting segments 92
selecting 91
Periodic Table 10
Perspectives, changing 167
PICT file format 188
PICT scaled 4x file format 188
Picture Layers
atom labels 73
Plain style, shapes 93
CambridgeSoft
ChemDraw 8
overview 19
Printing, contd.
page setup 165
paper size 166
PostScript atom labels 20
preferences 19
reaction mapping 158
Properties
atom in searching 137
atom, abnormal valence 142
atom, description 138
atom, implicit hydrogens 139
atom, query 137
atom, reaction changes 141
atom, reaction stereo 141
atom, resetting defaults 138
atom, ring bond count 140
atom, substituents 139
atom, unsaturation 140
atom, viewing values 138
bond 143
bond descriptors 143
bond types 144
bond, reaction center 145
bond, removing 143
bond, topology 145
bond, viewing 143
brackets 151
calculating 131
Proton shifts, see 13C, 1H shifts, estimating
Q
Quadruple bonds 53
Queries
multiple rings 150
Queries, see searching
Query indicators
editing 147
overview 147
Query Properties
3D 145
Query properties
exported 159
overview A10
Index
xiii
Administrator
Query Structures
description 137
exporting 159
Query Tools palette 147
Quick Reference Card, description 3
QuickDraw
bitmapped image 19
print quality 19
Quitting 20
R
R Groups 154
Racemic flag, drawing 148
Radicals
drawing 85
specification A7
Reaction Atom-Atom Map Tool 157
Reaction Atom-To-Atom Mapping 157
Reaction center 145
Reaction Changes 141
Reaction mapping
always display and print 158
automatic 158
clearing 159
exporting 159
manual 158
overview 157
Reaction Module in CAMEO/Excel 215
Reaction Parameters in CAMEO/Excel 215
Reaction Stereo 141
Reagent, Choosing a, in CAMEO/Excel 216
Red boxes on objects 61
Redo 16
Reduce
document window 163
object 167
page size 166
Reference numbers in MS Word 181
Reflection 103
Registration marks 164
Registration, online 196
Relative flag, drawing 148
Remove
colors 121
rulers 169
xiv
Index
CambridgeSoft
S
Sample code, SDK web site 197
Save As command 17
Save command
default file format 17
using 16
Saving
a copy of a document 17
changes automatically 15
defaults 13
document 16
in different file formats 17
structures in ChemDraw/Excel 205
template documents 125
with different name or location 17
Saving customized settings 13
Scale
command 104
dialog box 104
Scaling
by a percentage 104
fixed length 104
objects 104
when Transferring information 179
Scrap files 179
Script, Creating a in CAMEO/Excel 218
Script, Editing a in CAMEO/Excel 220
Script, Running a in CAMEO/Excel 221
Scripts menu 20
SDK A17
SDK Online, accessing 197
ChemDraw 8
Searching
ChemDraw/Excel 205
databases 137
export compatibility 159
online for chemical information 193
query properties supported 137
Select All command 99
Selecting
all 99
bonds 98
Lasso 97
last object 98
last tool 98
Marquee 97
Pen tool shapes 91
several objects 99
structures 98
Selection Rectangle
Resize handle 103
Rotation handle 101
Selection Tool
definition 6
deleting with Delete key 99
deselecting objects 99
distorting objects 105
highlight box 98
joining 105
Lasso 6
Marquee 6
selecting all 99
selecting several objects 99
using 97
Selection, adding to 99
Send to Back command 171
Set Color Button 119
Setting
margin width 73
preferences 12
Settings
document 12
highlight box 55
tolerance 55
Shaded style, shapes 93
Index
xv
Administrator
Shapes
closed 92
filled 92
plain 93
shaded style 93
Sharing Information 177
Shift key, deselecting objects 99
Show Crosshair 169
Show Page 167
Show Rulers command 168
Show Stereochemistry 129
Showing
Atom Numbering 77
palettes 8
sigma orbitals, drawing 82
Similarity searching
in ChemDraw/Excel 206
single bonds, drawing 52
Single brackets 88
skc format 186
SLN strings 178
SMD file format 188
SMILES
creating 177
overview 177
paste 178
viewing clipboard 177
SMIRKS, overview 177
Software Developers Kit A17
Solvent Information in CAMEO/Excel 216
s-orbitals, drawing 82
SPC file format 188
Spectra
assigning structures 134
exporting 187, 188
importing 187, 188
importing as JDX 187
importing as SPC 188
removing assignments 134
Spectrum-structure assignments
making 134
removing 134
viewing 134
Spiro linkage, templates 123
Squiggly Bond tool see Wavy Bond tool 52
xvi
Index
CambridgeSoft
Style sheet
Document settings 12
Style Sheets
color palette 121
creating A19
default 12
provided A19
Style, caption 66
Submitting a Reaction in CAMEO/Excel 215
Subscript command 66
Substituents 139
Substructure searching, in ChemDraw/Excel 205
Superatom, ISIS 186
Superscript command 66
Supplier, finding online 193
Suppress chemical warnings 21, 61
Syntax Checking 127
Synthesis/Synlett Document A20
System requirements 4
T
Table tool 172
Tables
column spacing 175
creating 174
creating with Table tool 172
inserting rows 175
moving in 175
Technical support A35
Template Panels 124
Template Tool
description 7
using 122
Templates
Autoscaling 122
coloring 121
creating 123, 124
drawing with 122
file format 188
fusing 123
fusing with existing structure 123
orientation 122, 124
overview 121
panel 124
resizing 124
ChemDraw 8
Templates, contd.
resizing template panes 124
reusing 123
saving template documents 125
spiro linkage 123
Text
atom label format 68
Atom label textbox 72
atom label, editing 73
atom labels, automatic justification 68
caption editing 71
caption, creating tables 174
coloring 70
creating 65
formatting 66
types 65
Text Box
closing 65
creating new line 65
Text Settings
captions, font, size, and style 69
changing defaults 13
Text Tool
atom labels 72
labeling atoms 72
toggling with lasso tool 76
Text tool 7
TGF file format 186
Thermal Capacity, calculation A14
TIFF
description 189
options 186, 189
resolution 186, 189
Tilting an object 105
Toggling
between tools 98
fixed length/fixed angle 54
text tool with lasso tool 78
Tolerance
effect on highlight box 98
setting 55
Tool
Alternative Group 154
Arrow 86
Reaction Atom-To-Atom Mapping 157
Index
xvii
Administrator
Tool, contd.
Templates 122
Text 65
Tools
Acyclic Chain 57
acyclic chain 7
Arc 89
arc 7
arrow 7
attachment point 155
benzene ring 55
bold bond 52
bold wedge bond 52
Bond 6, 52
Bracket 88
brackets 7
Chemical Symbol 84
chemical symbols 7
cyclohexane chair 55
cyclohexane ring 55
cyclooctane ring 55
cyclopentadiene ring 55
cyclopentane ring 55
cyclopropane ring 55
dashed bond 52
dative bond 52
Drawing Elements 87
drawing elements 7
eraser 6
hashed bond 52
hashed wedge bond 52
hollow wedge bond 52
Lasso 97
lasso 6
Marquee 97
marquee 6
mass fragmentation 133
multiple bond 52
Multiple bonds 6
Orbital 81
orbital 7
Pen 90
pen 7
Query 147
ring 7
xviii
Index
Tools, contd.
Structure perspective 6
Table 172
template 7
Text 7
Trackball 102
wavy bond 52
Topology 145
TPL style sheet 188
Trackball tool 102
Transferring information
across platforms 190
keeping in scale 179
Triple bond, drawing 53
Troubleshooting
online 196
Technical Support A36
Tutorial 21
Types of bonds A4
U
Undo 15
command 15
lost on save 15
Ungroup command 106
Ungrouping Objects 106
Unsaturation 140
Unspecified atom properties, in queries 139
Up to, in queries 139
Use Bitmap Fonts When Available 79
Use Defaults
atom properties 138
bond properties 143
Bracket properties 151
Preferences 12
Users guide, online 195
User-Defined Templates 123
Using the clipboard 100
V
Variable attachment command 115
Viewing
analysis information 128
atom properties 138
bond properties 143
CambridgeSoft
Viewing, contd.
chemical properties 131
Spectrum-structure assignments 134
Views
in ChemDraw/Excel 207
W
Warnings, chemical 61
Web site, CambridgeSoft, accessing 195
Wedge Bond, drawing 54
Whats New 1
White space, adjusting in atom labels 73
Window
analysis 128
chemical properties 131
Window menu
overview 18
stationery documents 14
Windows Help 3
Windows Metafile 188
WMF format 188
WWW, technical support A35
Z
Zooming, see Changing Perspectives
ChemDraw 8
Index
xix
Administrator
xx
Index
CambridgeSoft
Desktop Software
Enterprise Solutions
Research & Discovery
Applied BioInformatics
Knowledge Management
Chemical Databases
CAMBRIDGESOFT
ChemOffice Desktop to
KNOWLEDGE
MANAGEMENT
RESEARCH &
DISCOVERY
Desktop
E-Notebook
Enterprise
Discovery
LIMS
Registration
System
Document
Manager
21CFR11
Compliance
Formulations
& Mixtures
Inventory
Manager
Enterprise
WebServer
DESKTOP SOFTWARE
ChemOffice
Success begins at the desktop, where scientists use ChemDraw and ChemOffice to
E-Notebook
pursue their ideas and communicate with colleagues using the natural language of
ChemDraw
Chem3D
ChemFinder
ChemInfo
ChemOffice WebServer
Oracle Cartridge
chemical structures, models, and information. In the lab, scientists capture their
results by organizing chemical information, documents, and data with E-Notebook.
Chem3D modeling and ChemFinder information retrieval integrate smoothly with
ChemOffice and Microsoft Office to speed day-to-day research tasks.
ENTERPRISE SOLUTIONS
Just as ChemOffice supports the daily work of the individual scientist,
enterprise solutions and databases, built on ChemOffice WebServer, and Oracle
Cartridge help organizations collaborate and share information.
KNOWLEDGE MANAGEMENT
E-Notebook Enterprise
Document Manager
and available to others who need it. E-Notebook Enterprise streamlines daily record
Discovery LIMS
21CFR11 Compliance
keeping with rigorous security and efficient archiving, and facilitates searches by text
and structure. Document Manager organizes procedures and reports for archiving
and chemically-intelligent data mining. Discovery LIMS tracks laboratory requests, and
21CFR11 Compliance implements an organizations regulatory compliance processes.
SOLUTIONS
Enterprise Solutions
APPLIED
BIOINFORMATICS
CombiChem
Enterprise
Oracle Cartridge
or SQL DB
CHEMICAL
DATABASES
BioAssay
HTS
ChemACX
Database
The Merck
Index
BioSAR
Browser
ChemSAR
Properties
Chemical
Databases
Managing the huge data streams of new lab technology is a key challenge.
Inventory Manager
CombiChem Enterprise
organization's business rules, while Inventory Manager works with Registration System
and chemical databases for complete management of chemical inventories.
CombiChem Enterprise and Formulations & Mixtures are also important parts of
research data management.
APPLIED BIOINFORMATICS
BioAssay HTS
BioSAR Browser
biological assay data. Scientists use BioAssay HTS and BioSAR Browser to set up
biological models and visualize information, to generate spreadsheets correlating
structure and activity, and to search by structure.
CHEMICAL DATABASES
ChemACX Database
ChemSAR Properties
able ChemACX Database of commercially available chemicals. The Merck Index 13th
Edition and other databases provide necessary background about chemicals, their
properties, and reactions.
Consulting Development
CambridgeSoft's scientific staff has the industry experience, and chemical and
CS ChemOffice
So
ftw
ar
e
Software
Includes
*ChemDraw Ultra
Win/Mac
*ChemDraw Pro
Win/Mac
*ChemDraw Std
*ChemDraw Plugin Pro
Win/Mac
Win/Mac
*Chem3D Ultra
Win
*Chem3D Pro
Win
Chem3D Std
Win
Win
Win
Win
Win
ChemDraw/Spotfire
*BioAssay Pro
Purchase/Excel
CombiChem/Excel
Win
Win
Win
Win
ChemFinder/Office
Win
ChemDraw/Excel
Databases
Su
ite
s
Ch
em
O
ffi
ce
Win
Name=Struct
Struct=Name
Win/Mac
Win/Mac
ChemNMR
CLogP/ChemDraw
Win/Mac
Win/Mac
BioArt
Structure Clean Up
Win/Mac
Win/Mac
Polymer Draw
Win/Mac
LabArt
Win/Mac
ChemSAR/Excel
Win
3D Query
MOPAC/Chem3D
GAMESS Client
Gaussian Client
Win
Win
Win
Win
Tinker/Chem3D
Win
*CAMEO/ChemDraw
Win
Win
Win
Win
Win
Win
ChemRXN
Win
Win
*Available Separately
ECh
N
Ch
Ch
Ch
em
Ch
ot
em
e
e
eb
m
e
D
m
m
O
r
D
oo
D
a
3D
ra
ffi
ra
w
k
c
w
w
e
Ul
Ul
U
Ul
ltr
St
Pr
Pr
tra
tra
tra
d
a
o
o
ChemOffice Ultra
ChemOffice Pro
ChemDraw Ultra
ly available chemicals, The Merck Index 13th edition, and other databases.
Consulting & Services includes consulting development, technical
E-Notebook Ultra
DESKTOP
CS E-Notebook
Electronic Journal and Information
E-Notebook Ultra streamlines daily record keeping tasks of research scientists, maintains live chemical
structures and data, and saves time documenting work and retrieving chemical information. E-Notebook combines all of your notebooks into one and sets up as many project notebooks as you need, organized the way you
work. Notebook pages include ChemDraw documents, Excel spreadsheets, Word documents and spectral data.
E-Notebook automatically performs stoichiometry calculations on ChemDraw reaction pages. Search by structure, keyword, dates and other types of data. Maintain required hardcopy archives by printing out pages.
Information cannot be accidentally modified. Spectral controls from Thermo Galactic are available.
CombiChem/Excel builds combinatorial libraries with embedded ChemDraw structures using
ChemDraw/Excel for Windows. Find reagents with ChemFinder and design experiments.
BioAssay Pro, available in ChemOffice Ultra, allows for flexible storage and retrieval of biological data. It
is designed for complex lead optimization experiments and supports almost any biological model.
Automatic
Stoichiometric
Calculations
Scanned Images in
Notebook Pages
S O F T WA R E
E-Notebook Ultra
CombiChem/Excel
Combinatorial Chemistry in Excel
Generate combinatorial libraries
Choose starting materials & reaction schemes
View structures & track plate/well assignments
ChemFinder Pro
Premier Searching & Information
Advanced search & structure query features
Stores structures & reactions along with calculated data & associated information
Search by substructure including stereochemistry using ChemDraw
Integration with ChemDraw & Chem3D
Import/export MDL SD & RD files
ChemInfo Std
Reference & Reaction Searching
ChemINDEX for small molecule information
ChemRXN for reaction databases
BioAssay Pro
Biological Assay Structure Activity
Set up biological models & visualize information
Search data by structure to isolate key structural determinants of biological activity
Tabulate & analyze structure-activity relationships with spreadsheet templates
Available in ChemOffice Ultra
SYSTEMS & LANGUAGES
English & Japanese
Windows: 95, 98, Me, NT, 2000, XP
This software is Windows only.
All specifications subject to change without notice.
DESKTOP
CS ChemDraw
Chemical Structure Drawing Standard
ChemDraw Ultra adds ChemDraw/Excel, ChemNMR, Name=Struct, Beilsteins AutoNom, CLogP and
ChemFinder/Word to ChemDraw Pro. With rich polymer notation, atom numbering, BioArt templates, and
modern user interface, ChemDraw is more powerful than ever before. Create tables of structures, identify and
label stereochemistry, estimate NMR spectra from a ChemDraw structure with structure-to-spectrum
correlation, obtain structures from chemical names, assign names from structures, and create multi-page
documents and posters.
ChemDraw Pro will boost your productivity more than ever. Draw publication-quality structures and
reactions. Publish on the web using the ChemDraw Plugin. Create precise database queries by specifying atom
and bond properties and include stereochemistry. Display spectra, structures, and annotations on the same
page. Use the Online Menu to query ChemACX.Com by structure, identify available vendors, and order online.
Stereochemistry
Structure-to-Spectrum
NMR Correlation
S O F T WA R E
ChemDraw Ultra
ChemDraw Pro
Premier Drawing & Information Query
Query databases precisely by specifying atom & bond properties, reaction centers,
substituent counts, R-groups & substructure
Read ISIS files with Macintosh/Windows cross-platform compatibility
Structure Clean Up improves poor drawings
Display spectra from SPC and JCAMP files
Chemical intelligence includes valence, bonding & atom numbering
Right-button menus speed access to features
ChemDraw Std
Publication Quality Structure Drawing
Draw and print structures & reactions in color,
and save as PostScript, EPS, GIF, SMILES & more
Collections of pre-defined structure templates
Large choice of bonds, arrows, brackets, orbitals, reaction symbols & LabArt
Style templates for most chemical journals
Compatible with Chem3D, ChemFinder, ChemInfo, E-Notebook & Microsoft Office
ChemDraw Plugin
Advanced WWW Structure Client
Embed live ChemDraw documents in WWW pages
Works with Netscape & Internet Explorer
Included with ChemDraw Ultra & Pro
SYSTEMS & LANGUAGES
Windows & Macintosh English, Japanese, French, German
Windows: 95, 98, Me, NT, 2000, XP
Macintosh: MacOS 8.6-10.1
Some features are Windows only.
All specifications subject to change without notice.
DESKTOP
CS Chem3D
Molecular Modeling and Analysis
Chem3D Ultra includes MOPAC, Tinker and set-up/control interfaces for optional use of GAMESS and
Gaussian. Estimate advanced physical properties with CLogP and ChemProp, and create SAR tables using
property servers to generate data for lists of compounds. Use ChemSAR/Excel to explore structure activity
relationships and use add-on Conformer for conformational searching. Publish and view models on the web
using the Chem3D Plugin.
Chem3D Pro brings workstation quality molecular visualization and display to your desktop. Convert
ChemDraw and ISIS/Draw sketches into 3D models. View molecular surfaces, orbitals, electrostatic potentials,
charge densities and spin densities. Use built-in extended Hckel to compute partial atomic charges. Use MM2
to perform rapid energy minimizations and molecular dynamics simulations. ChemProp estimates physical
properties such as logP, boiling point, melting point and more. Visualize Connolly surface areas and
molecular volumes.
Large Molecular
Visualization
S O F T WA R E
Chem3D Ultra
Chem3D Pro
Premier Modeling, Visualization & Analysis
Create 3D models from ChemDraw or ISIS Draw, accepts output from other modeling packages
Model types: space filling CPK , ball & stick, stick, ribbons, VDW dot surfaces & wire frame
Compute & visualize partial charges, 3D
surface properties & orbital mapping
Polypeptide builder with residue recognition
ChemPropBasic property predictions with Connolly volumes & surface areas
MM2 minimization & molecular dynamics, extended Hckel MO calculations
Supports: PDB , MDL Molfile, Beilstein ROSDAL, Tripos SYBYL MOL , EPS , PICT , GIF , 3DMF , TIFF , PNG & more
MOPAC/Chem3D
Advanced Semi-Empirical Computation
Calculate Hf, solvation energy, dipoles, charges, UHF & RHF spin densities, MEP , charge densities & more
Optimize transition state geometries
AM1 , PM3 , MNDO & MINDO/3 methods
CAMEO/ChemDraw
Synthetic Reaction Prediction
Expert system predicts and displays products
ChemDraw creates starting materials when you choose reaction conditions; sold separately
Chem3D Plugin
Advanced WWW Model Client
Works with Microsoft Internet Explorer
Visualize 3D molecules on ChemFinder.Com
SYSTEMS & LANGUAGES
Windows & Macintosh English & Japanese
Windows: 95, 98, Me, NT, 2000, XP
Macintosh: MacOS 8.6-9.2.X
Some features are Windows only.
All specifications subject to change without notice.
DESKTOP
CS ChemFinder
Searching and Information Integration
ChemFinder Pro is a fast, chemically intelligent, relational database search engine for personal, group or
enterprise use. Extended integration with Microsoft Excel and Word adds chemical searching and database
capability to spreadsheets and documents.
An ever-increasing number of chemical databases are available in ChemFinder format. Compatibility with MDL
ISIS databases is provided by SDfile and RDfile import/export. ChemFinder provides network server workgroup
functionality when used with ChemOffice WebServer.
ChemFinder/Word is an extension of Microsoft Excel and Word for Windows. Create structure searchable spreadsheets and index documents with embedded ChemDraw structures.
ChemDraw/Excel adds chemical intelligence to Microsoft Excel for Windows. Show structures in spreadsheet cells, tabulate chemical calculations and analyze data with Excel functions and graphs.
Purchase/Excel uses ChemDraw/Excel to manage reagent lists and track purchasing information.
CombiChem/Excel builds combinatorial libraries with embedded ChemDraw structures using
ChemDraw/Excel for Windows. Find reagents with ChemFinder and design experiments.
ChemDraw/Excel
Search Chemical
Databases
S O F T WA R E
ChemFinder/Word
Search structures in documents & folders
ChemDraw/Excel
Add chemical intelligence to spreadsheets
Purchase/Excel
Organize chemical purchasing information
ChemFinder Pro
Premier Searching & Information
Advanced search and structure query features
Stores structures and reactions along with calculated data and associated information
Search by substructure including stereochemistry using ChemDraw
Import/export MDL SD and RD files
Integration with ChemDraw and Chem3D
ChemFinder/Word
Searching Word, Excel & More
Searches documents for embedded structures
Indexes structures and source locations
Searches specified folders and whole hard drives
ChemDraw/Excel
Searching & Calculating in Excel
Displays ChemDraw structures in spreadsheet cells
Adds chemical calculations to Excel functions
Useful for graphing and analyzing chemical data
Purchase/Excel
High Throughput Purchasing
Finds vendor and price information from ChemACX Database or ChemACX.Com
Search for suppliers and purchase online
Maintains lists of compounds
CombiChem/Excel
Combinatorial Chemistry in Excel
Generate combinatorial libraries
Choose starting materials and reaction schemes
View structures and track plate/well assignments
SYSTEMS & LANGUAGES
English & Japanese
Windows: 95, 98, Me, NT, 2000, XP
This software is Windows only.
All specifications subject to change without notice.
EMAIL info@cambridgesoft.com WWW www.cambridgesoft.com
TEL
1 800 3157300
INTL 1 617 5889300
FAX 1 617 5889390
MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge, MA 02140 USA
ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft 2002.
All other trademarks are the property of their respective holders. All specifications subject to change without notice.
DESKTOP
CS ChemInfo
Reference and Chemical Databases
The Merck Index is an encyclopedia of chemicals, drugs, and biologicals, with over 10,000 monographs
covering names, synonyms, physical properties, preparations, patents, literature references, therapeutic uses
and more.
ChemACX Pro includes 500,000 chemical products from 300 supplier catalogs, searchable with a single
query by structure, substructure, name, synonym, partial name, and other text and numeric criteria.
ChemACX-SC is a compilation of searchable catalogs from leading screening compound suppliers.
ChemACX.Com is the ChemACX web site with full search capabilities and convenient online ordering
from major suppliers.
ChemINDEX includes 100,000 chemicals, public NCI compounds, and more.
ChemRXN is a collection of 30,000 fully atom-mapped reactions selected and refined from the chemical
literature. It includes reactions from InfoChems ChemSelect database and ISI s ChemPrep database.
ChemMSDX provides material safety data sheets for 7,000 pure compounds.
ChemFinder.Com is the award-winning web site with information and WWW links for over 100,000
chemicals. Search by name or partial name, view structure drawings, or use the ChemDraw Plugin for structure
and substructure searches. View live ChemDraw files on Windows and Macintosh clients.
ChemRXN database
on CD-ROM
ChemINDEX database on
ChemFinder.Com
S O F T WA R E
The Merck Index
Encyclopedic chemical reference
ChemACX Pro
Chemical searching & buying
ChemACX Pro
Chemical Searching & Buying
Database of commercially available chemicals: 300 catalogs with 500,000 chemical products
ChemACX-SC database with 500,000 structures from leading screening compound suppliers
ChemACX.Com
WWW Chemical Searching & Buying
Search by text, structure or substructure and order online from major catalogs
ChemINDEX
Reference Searching & Information
NCI database of over 200,000 molecules, with anti-HIV & anti-cancer assay data
ChemRXN
Reaction Searching & Information
Includes ChemSelect with reactions from InfoChem GmbH & ISIs ChemPrep
ChemMSDX
Safety Data Searching & Information
Provides full Material Safety Data Sheets for over 7,000 pure compounds
ChemFinder.Com
WWW Reference Searching & Info
WWW links for over 100,000 compounds
Enter text queries or use ChemDraw Plugin for structure & substructure searching
Works with Netscape & MS Internet Explorer
SYSTEMS & LANGUAGES
English & Japanese
Windows: 95, 98, Me, NT, 2000, XP
CD-ROM software is Windows only.
All specifications subject to change without notice.
ENTERPRISE
ChemOffice WebServer
Enterprise Solutions, Applications and Databases
ChemOffice WebServer
ChemOffice WebServer is the leading solution platform for enterprise, corporate intranet, and Internet scientific information applications. Compatible with major databases including Oracle, SQL Server, and Microsoft
Access, ChemOffice WebServer is the development and deployment platform for custom applications and those
listed below.
ChemOffice Browser
ChemOffice Browser, including ChemDraw Java, ActiveX, and the ChemDraw and Chem3D Plugins, brings the
power and chemical intelligence of ChemOffice to Internet and intranet applications.
User Friendly & IT Ready
User-friendly and IT ready ChemOffice WebServer and Browser enterprise solutions, applications and databases are easier and faster for users to learn and the IT staff to deploy. Using ChemOffice WebServer technology,
along with familiar browser technology, overall costs are lowered and less time is required for implementation.
Enterprise Solutions
Enterprise solutions built upon ChemOffice WebServer, including Oracle Cartridge, help workgroups and
organizations collaborate and share information, just as ChemOffice supports the daily work of the scientist.
Browse Detailed
Compound Information
Easy Management
of Search Results
SOLUTIONS
Knowledge Management
Knowledge Management applications organize and distribute chemical information. E-Notebook Enterprise
streamlines daily record keeping with rigorous security and efficient archiving, and facilitates information
retrieval by structure and text searching. Document Manager indexes the chemical structure content of documents, Discovery LIMS tracks laboratory requests, and 21CFR11 Compliance implements an organizations regulatory compliance processes.
Research & Discovery
Research and discovery applications include Registration System for managing proprietary compound information, Inventory Manager for reagent tracking needs, and chemical databases for complete management of chemical inventories. Formulations & Mixtures and CombiChem Enterprise also provide tailored approaches to managing chemical data.
Applied BioInformatics
BioAssay HTS and BioSAR Browser applications process biological assay data to pinpoint the structural determinants of biological activity. BioAssay HTS supports low, high, and ultra-high throughput workflow, including sample and plate management, while BioSAR Browser probes structural details within assay data.
Chemical Databases
The Merck Index and ChemACX Database provide reference information, property estimations, and searchable
compilations of commercially available chemicals.
ENTERPRISE
Oracle Cartridge
Simple Client-Server
Architecture
Web Based
Architecture
SOLUTIONS
KNOWLEDGE
E-Notebook Enterprise
Desktop to Enterprise Knowledge Management
E-Notebook
E-Notebook provides a smooth web-based interface designed to replace paper laboratory notebooks, with a fully
configurable, secure system for organizing the flow of information generated by your organization. You can enter
reactions, Microsoft Word documents, spectra and other types of data, and then search this data by text, substructure or meta-data. You can organize your electronic pages by projects, experiments or any other classification that conforms to your workflow.
Desktop to Enterprise
E-Notebook allows organization of notebook pages at either the personal or enterprise level. Enterprise groups can
organize and store notebook pages in a central data repository, allowing colleagues to take advantage of each
others work. All access to data is subject to granular security. E-Notebook works with Oracle Cartridge and SQL
Server, for departments or entire enterprises, and Microsoft Access, for individuals or small groups.
ChemDraw & Stoichiometry Calculations
While not quantum theory, stoichiometric calculations remain long and tedious. E-Notebook tackles this troublesome problem. First, draw your reaction directly in the page. Then, simply enter the mass, volume and denAutomatic Stoichiometric Calculations
Scanned Images in
Notebook Pages
MANAGEMENT
sity, volume and molarity, and other factors of the limiting reagent and specify the number of equivalents of the
other reactants. The notebook will do everything except calculate the experimental yield. To do that, you still
have to run the experiment!
Microsoft Office & Galactic Spectra
E-Notebook manages all the other kinds of data chemists store in their notebooks. For free-form data, you can
include Microsoft Word or Excel documents. For spectral data, you can take advantage of the Galactic Spectral
Control embedded in the notebook that allows for analysis and storage of hundreds of kinds of spectra files.
Inventory Manager
E-Notebook includes an inventory of common reactants and reagents. If you have one of these common components loaded into the inventory application, all you have to do is click the Add Reactant button in
E-Notebook. From here, you navigate to the desired compound and include it in your stoichiometry calculations. The enterprise edition of E-Notebook integrates with procurement and inventory management systems.
Not only does this provide a useful way to know what compounds you have in stock and where they are located, it also saves time entering data.
Registration System
E-Notebook can be integrated into the entire chemical workflow of enterprise organizations. For example, once
you record a reaction in your notebook, you can click a button to forward the products of the reaction to your
compound registration system. These kinds of workflow enhancements increase productivity for the entire
organization.
KNOWLEDGE
Document Manager
Desktop to Enterprise Document Searching
Document Manager
Everyone produces reports electronically, but searching information located in these reports has always been
difficult. Thousands of Microsoft Word, Excel, PowerPoint, and other documents reside on file servers or individual computers, with no way to globally search them for information. Certainly, no easy way exists to search
for the chemistry contained in these documents. Document Manager solves this problem, and requires no
change in how you write and distribute reports.
Easy to Use
Document Manager manages a repository of new documents. These can be Microsoft Word, Excel, PowerPoint,
or many other document types. When a new document is added, Document Manager automatically builds a
free-text index of the document, and automatically extracts the chemical information into a chemically-aware,
substructure searchable database. Chemical information can be both ChemDraw and ISIS /Draw. Finding information in reports is now as simple as entering a query through your web browser.
Unattended Data Indexing
As new documents are added they are automatically indexed and chemical information is extracted. Similarly, if
a document is modified, it is re-indexed. No administration of the server is necessary other than routine back-up.
Unattended Data
Repository Indexing
Search Documents
by Structure
MANAGEMENT
KNOWLEDGE
21CFR11 Compliance
Electronic Records and Signatures Regulations
The Challenge
Large and growing enterprises are facing a challenge to their core missions of developing and producing new
products including food, therapeutic pharmaceuticals, medical devices, cosmetics or other health enhancing
items. The complexity lies in complying with government regulations designed to protect public health and
safety. The most notable of these is Title 21 of the Code of Federal Regulations governing Electronic Records
and Signatures (21CFR11). Although 21CFR11 has been in the draft stage for almost a decade, final regulations have recently been created. Enforcement of these regulations is beginning to take place and enterprises are
responding with a wide variety of initiatives, both within individual organizations and across industry sectors.
Integrated Software
CambridgeSoft applications, such as E-Notebook Enterprise and Document Manager, are at the leading edge of
the integration of corporate knowledge management with 21CFR11 Compliance. These products are designed so
that as your organization reviews its internal processes for 21CFR11 Compliance, the software can be configured
to support these internal processes. Major requirements of 21CFR11, such as electronic signatures, audit trails,
and long-term archiving, are incorporated within the routine workflow to generate the critical information
required by research, development and production. In addition, E-Notebook Enterprise and Document Manager
can be integrated with existing critical data systems.
Document and
Record Management
MANAGEMENT
Analysis
As your enterprise develops the operating procedures that you will need to adopt for 21CFR11 Compliance,
CambridgeSofts consulting team can provide invaluable assistance in analyzing your current operating procedures, adapting your existing procedures to comply with new regulations, and validating the software and the
operating procedures that you will use. CambridgeSofts consulting teams consist of individuals who have
extended experience in deploying systems used by large pharmaceutical companies, emerging biotechs, and
major enterprises worldwide.
Implementation
Once you have determined how your enterprise will comply with these new regulations, implementing those
decisions needs to be done quickly, efficiently and with the understanding that the rules for compliance are in
flux. In order to succeed, you must be able to respond to change. CambridgeSofts 21CFR11 Compliance consulting has both the tools and the expertise to provide complete solutions, carry out integration with your existing systems, and help you execute the process as quickly as your organization demands. Since ongoing monitoring is a part of business for regulated industries, you can be confident that, as regulations evolve and your
requirements change, your systems can adapt. With CambridgeSoft, you can take advantage of the knowledge
that has helped dozens of businesses, large and small, gain control over their business processes, their
intellectual capital, and their material resources.
RESEARCH &
Registration System
Registration System includes a robust data model for pure compounds, batches, salt management, automatic
duplicate checking and unique ID assignments. Compounds may be entered individually or with SD files. The
data model resides entirely in Oracle and uses Oracles security and transaction framework. For companies
intending to modify or construct their own registration system, ChemOffice WebServer includes a powerful
Software Developers Kit (SDK ) to add custom functionality. Instead of inventing a proprietary language,
ChemOffice WebServer SDK extends the Microsoft and Oracle platforms, allowing information scientists to use
the industrys most powerful development tools.
ChemDraw Plugin & WebServer
Registration System is easily adapted in almost any work environment. Its web-based, industry standard
ChemDraw interface, makes ChemOffice WebServer the best choice for your corporate scientific information.
User Friendly Chemical Registration
New compounds are entered through a web form, and chemical, along with non-chemical, data is kept in a
temporary storage area. When the compound is registered, it is compared for uniqueness via a configurable,
stereoselective duplicate check, and assigned a registry number. All information about the compound, including its test data and other syntheses, is tracked by the registry number.
Display & Format Results
DISCOVERY
RESEARCH &
Inventory Manager
Database Technology
Inventory Manager is a ChemOffice WebServer based application designed to manage the reagent tracking needs of
chemical and pharmaceutical research centers. The system manages data associated with both commercially
and internally produced chemical substances. Although Inventory Manager is a stand-alone application, it can
be tightly integrated with CambridgeSofts Registration System and chemical procurement ChemACX Database.
Inventory Manager is designed for a range of sizes from large workgroups to enterprises, and captures both
stockroom and reagent needs as well as high-throughput discovery.
Cascading Location Model
Inventory Manager has a fully cascading location model. This means that laboratories can decide for themselves
the granularity of their locations. Some labs may define locations as wells on plates residing on shelves inside
refrigerators, which, in turn, are found in laboratories. Another lab may decide to track reagents at the bench
or cabinet level. Still, in other settings, it may suffice to track chemicals on a lab-by-lab basis. The moving of
chemical inventories is greatly helped by this model. For example, if an entire refrigerator is relocated, all of its
containers move along with it. There is no need to re-catalog or reconcile, which saves a great deal of time.
Substructure Search
Form
Viewing Information
by Container
DISCOVERY
RESEARCH &
CombiChem Enterprise
Desktop to Enterprise Combinatorial Chemistry
Reaction Based
Library Generation
Library in
Spreadsheet View
DISCOVERY
Finding Reagents
Flexibility is the key when dealing with databases of chemical compounds. CombiChem Enterprise can use
reagent lists from a variety of different sources: SD files, ChemFinder databases, ChemFinder hit lists, ChemOffice
WebServer hit lists, ChemACX Database, or directly from the user via ChemDraw. Regardless of the source,
CombiChem Enterprise produces a list of reagents which match a particular generic reactant. The chemist then
chooses which of the compounds to use for generating products.
Getting Results
Once the chemist has given CombiChem Enterprise a set of reagents for each of the generic reactants in the
reaction scheme, the software generates the set of products which would result from running the experiment.
CombiChem Enterprise evaluates the products using several in silico methods, and the chemist can then choose
which compounds to keep and which ones to reject. After the products have been generated, the software
provides product information for each of the reagents. The chemist can use that information, for example, to
trim away reagents having few or no products which pass the Lipinski Rule of Five test. Finally, the products
are laid out on plates based on user-definable plate layouts.
Integration with E-Notebook
Keeping track of compound library data can be a challenge: which reagents led to this product, which
product goes with that spectrum, what was in the mixture used in this thin layer chromatography? CombiChem
Enterprise provides ways to organize the data and navigation is simple. When used with E-Notebook Enterprise,
the data for a library of shared compounds, and the entire experiment, is automatically documented and made
available to the entire organization.
RESEARCH &
BioAssay HTS
BioAssay HTS
BioAssay HTS provides scientists with an effective way of managing test results for biological and other kinds
of experiments intended to assess the efficacy of compounds. Suitable for both plate-based high throughput
screening assays and smaller-scale lead optimization experiments, BioAssay HTS provides researchers with
simple tools for setting up their models in a database, uploading data, automating calculations and reporting
on their findings.
User Friendly Assay Management
Even for the most basic protein assays, the independent and dependent variables used by the biologist to quantify efficacy can vary substantially from assay to assay. The underlying requirement that follows from this variability is for a flexible data management system that can adapt quickly to different assays and biological models. With BioAssay HTS, researchers or IT support staff simply define the observables and calculations that
make up the assay. The database does the rest. Users can set up unlimited levels of drill-down. This allows users,
for example, to click an IC50 and see a graph of percent inhibition versus concentration. Click again, and the
software displays the original triplicate results, with outliers marked. The software even supports complex in
vivo models.
Automated Curve
Fitting & Data Analysis
Flexible Assay
Definition Tools
DISCOVERY
RESEARCH &
BioSAR Browser
Biological and Chemical Meta Data Catalog
BioSAR Browser
BioSAR Browser, a strategic must for any discovery organization interested in serious data mining, is a data-dictionary driven structure-activity analysis program. Users may choose among assays registered in the dictionary or
search for assays of interest.
Providing Catalog Capabilities
The power of BioSAR Browser lies in the researchers freedom from dependence on IT support. Once an assay
is registered into the data-dictionary it is automatically included in the powerful analysis framework. By reducing the time between question and answer, BioSAR Browser gives researchers the freedom to explore new
ideasthe bottom line for discovery information systems. Systems that provide answers after questions have
become irrelevant are of no use. BioSAR Browser avoids this by placing application development in the
researchers control.
Forms & Tables in a Unified Interface
While most SAR tools provide only a table-based interface, BioSAR Browser provides a forms-based interface in
addition to a tabular view. Researchers have demonstrated that both form and tabular views are essential. Forms
provide highly detailed information about one compound, whereas tabular views make comparisons between
Data Dictionary
Organizes Reports
DISCOVERY
compounds more feasible. There is often a tradeoff between power and simplicity, and most SAR tools opt for
the former at the expense of the latter. BioSAR Browser, however, merges the sophistication of a powerful data
catalog technique with knowledge gained through years of working closely with users. The result is a SAR
application that is as intuitive as it is powerful.
Security & Convenience
Security within BioSAR Browser is highly granular. Different roles exist for administrators, publishers, and
browsers. Administrators may add assays to the data catalog engine, publishers may create reports and publish
them, and browsers may use data query and analysis. Most data mining tools provide a mechanism to store
queries, but the interface for creating queries is too complex. With BioSAR Browser, each set of assays is a complete report with a query form, a view form, and a table view, combining the convenience of a ChemFinder or
ISIS application with the power and flexibility of a data catalog-driven mining program.
ChemDraw for Spotfire
ChemDraw for Spotfire is a powerful add-in for the Spotfire DecisionSite software. Spotfire makes industry
standard applications for high-dimensional visual data analysis, and is used to explore large biological datasets.
ChemDraw for Spotfire adds chemistry to DecisionSite, providing structure visualization and searching services. Highlight a spot in Spotfires DecisionSite, and a structure is displayed directly in the window. If you draw
a structure and click Search, the matching records are displayed right in the Spotfire window. The structures
are retrieved from a chemical database such as Registration System, ChemFinder, or Oracle Cartridge, and are
returned directly over the network. In this way, structures can be linked by registry number, CAS number, or
CHEMICAL
ChemACX Database
ChemACX Database
Sifting through chemical catalogs is a poor use of time for any researcher. The Available Chemicals Xchange
database, ChemACX Database, provides a complete tool for research chemical sourcing and purchasing. The
database can be accessed from both desktop and enterprise environments and boasts an impressive list of major
suppliers, from Alfa Aesar and Aldrich, to TCI and Zeneca with hundreds in between. The enterprise procurement solution for ChemACX saves time by streamlining the entire purchasing process. Use ChemACX to
build an internal requisition, print the form on your company template, fill it out and submit it to purchasing.
ChemACX-SC
ChemACX-SC is an additional fully structure searchable database containing the catalogs of leading screening
compound suppliers, including ChemBridge, Maybridge, Sigma-Aldrichs Rare Chemical Library and others.
Data Quality
Over 500,000 products from 300 research chemical and biological catalogs have been selected to have their
product catalogs prepared for electronic delivery. The data provided by the suppliers is enriched by editors who
add searchable chemical structures, physical and chemical properties, and incorporate a comprehensive
chemical synonym dictionary. All substances and supplier catalog numbers are cross-referenced, making it easy
to locate alternate sources for back ordered or discontinued items.
ChemACX on CD-ROM
D ATA B A S E S
Data Currency
A premium is placed on the accuracy and currency of the ChemACX Database. Many suppliers listed in the
database are also currently selling their products online through the ChemACX.Com web site, and therefore
have a vested interest in ensuring that their data remains complete, accurate and up-to-date. You wont find a
sourcing database with more frequently updated content and current pricing than ChemACX.
Data Accessibility
The same way that Internet users can publicly access ChemACX.Com, enterprise users can access their private
ChemACX Database via a standard web browser. There is no need to configure or install any additional software. ChemDraw users can either use the ChemDraw Plugin to draw chemical structures directly in the browsers search page, or alternatively submit queries to the database server directly from ChemDraw. ChemFinder
users can access their own copy of the database right from their local hard drive.
Electronic Requisitions
Traditional sourcing databases were conceived merely as reference tools. ChemACX Database, however, goes
one step further by including the ability to collect products into an electronic shopping cart and export its contents into electronic requisition forms or purchasing systems. This time-saving feature has proven to be one of
the most popular advantages of ChemACX among scientists and purchasing agents alike. Users can readily
export data from the shopping cart into Excel and Word templates used as departmental requisition forms.
CHEMICAL
Industry Standard
Among printed chemical reference works, one that stands out for its integrity, detail and longevity is The Merck
Index. This encyclopedia of chemicals, drugs and biologicals has 10,250 monographs, 446 named reactions and
23 additional tables. Merck & Co., Inc., the publisher of The Merck Index, has chosen CambridgeSoft to produce the complete contents of the 13th edition in a fully searchable ChemOffice format.
Detailed Monographs
The subjects covered include human and veterinary drugs, biologicals and natural products, agricultural chemicals, industrial and laboratory chemicals, and environmentally significant compounds. What makes The
Merck Index so valuable is its extensive coverage. The information provided includes chemical, common and
generic names, trademarks, CAS registry numbers, molecular formulas and weights, physical and toxicity data,
therapeutic and commercial uses, and literature citations. In addition to the standard searches, compound
monographs can now be searched by ChemDraw structure as well as substructure. Moving this information to
the fully searchable ChemOffice format makes it easier and faster to search and get results. Instead of consulting the auxiliary indices and then turning to the actual monograph, all searching can be done from a single form.
D ATA B A S E S
Integrated Information
Having The Merck Index in ChemOffice format confers another valuable benefit: integration with other information sources. For example, after locating a substance in The Merck Index, it is a simple matter to copy the
name, structure or other data elements to search ChemACX Database to find out whether there are commercial
suppliers of the substance. The structures could also be used as input to Chem3D to obtain three-dimensional models and to perform electronic structure and physical property calculations. Information can also be brought
into any ChemOffice desktop or enterprise solution, including ChemDraw/Excel, ChemFinder/Word, E-Notebook
and Registration System.
ChemOffice Formats
The Merck Index is available in two ChemOffice compatible formats. The desktop edition is a CD-ROM in a
ChemFinder database format, for use by an individual researcher. The enterprise edition, designed for workgroups
and larger user communities, is served by ChemOffice WebServer to connected users. The Merck Index thus adds
to the growing set of reference databases served by ChemOffice WebServer. Just as ChemOffice integrates the
desktop edition of The Merck Index with the scientists everyday activities, the enterprise edition becomes an integral part of the applications deployed on ChemOffice WebServer.
Web Versions
The complete contents of The Merck Index are also available online through your favorite web browser. To
meet your specific needs, single user subscriptions, corporate extranet subscriptions and intranet webservers are
all available.
CHEMICAL
Chemical Databases
Databases
ChemOffice WebServer provides a full range of compound and reaction databases essential for research.
Databases are available at ChemFinder.Com, or over corporate intranets.
Reference
The Merck Index contains encyclopedic references for over 10,000 chemicals, drugs and biologicals.
ChemINDEX includes 100,000 chemicals, public NCI compounds and others.
World Drug Index (WDI ) from Derwent contains over 58,000 compounds with known biological activity.
WDI classifies compounds according to type of biological activity, mechanism, synonyms, trade names,
references and more.
Chemicals
ChemACX and ChemACX-SC, Available Chemicals Xchange, is a large and growing source for information
on compound availability. It lists compounds from Alfa Aesar and Aldrich to TCI and Zeneca with hundreds
in between, including 500,000 products from 300 catalogs. ChemACX-SC is a library of screening compounds.
ISI Reactions
Derwent Patents
D ATA B A S E S
Reactions
Organic Syntheses is the electronic version of the annual and collective volumes of trusted, peer reviewed synthesis procedures published since 1921 by Organic Syntheses.
Current Chemical Reactions (CCR) from ISI is both a current awareness and a data mining application used to
design chemical syntheses. Renowned for its quality, CCR contains information from over 300,000 articles
reporting the complete synthesis of molecules. Updated daily, CCR is an excellent way to stay on top of recent
developments.
ChemReact and ChemSynth from InfoChem are carefully selected from a database of over 2.5 million reactions through an automated process of reaction classification. With over 390,000 reaction types, ChemReact is for
expert synthetic chemists designing novel syntheses. Entries in ChemSynth are further refined to those with over
50% yield and at least two literature references.
ChemRXN is a refined selection of over 29,000 fully atom-mapped reactions. Including carefully selected reactions
from InfoChems ChemSelect database and ISIs ChemPrep database, ChemRXN is a terrific combination of utility.
Patents
World Drug Alerts (WDA) from Derwent is a current awareness application providing information on patents,
new biologically active compounds, new methods for synthesizing drugs, and other data. It is a requirement for
effective decision making in all stages of drug design.
Investigational Drugs Database (ID db) from Current Drugs is the worlds leading competitor intelligence
service on drug R&D. Updated weekly, it covers all aspects of drug development world wide, from first patent to
launch or discontinuation.
Safety MSDS
ChemMSDX provides over 7,000 material safety datasheets.
EMAIL info@cambridgesoft.com WWW www.cambridgesoft.com
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FAX 1 617 5889390
MAIL CambridgeSoft Corporation 100 CambridgePark Drive Cambridge, MA 02140 USA
ChemOffice, ChemDraw, Chem3D, ChemFinder & ChemInfo are trademarks of CambridgeSoft 2002.
All other trademarks are the property of their respective holders. All specifications subject to change without notice.
C O N S U LT I N G &
Managing Information
Todays businesses are facing many complex issues. Among them are the overloads of disparate types of information, unmanaged proliferation of valuable research data, virtual projects in many locations, uncontrolled
research data, compliance, certification and regulation. Technological solutions to these issues require careful
planning and management. CambridgeSoft now offers the following professional services to assist businesses
in fully utilizing the power of technology.
Decision Making
CambridgeSoft believes that successful technology utilization begins with the assessment and decision making
process. Our experts can assist clients with:
Readiness Assessment: Identify the scope, requirements, and deliverables for your project. Assure critical IP
is incorporated. Allow end-users to capitalize on existing scientific and technology resources.
Strategic Planning: Conduct formal analysis of scientific, technical, operational, and process environments
to determine the necessary approach to customization and deployment.
Prototypes and Proof of Concept: Prototypes allow you to test the technical feasibility of solutions. This
activity can provide a baseline for the future roll-out of the solution, and can also gather user feedback so
requirements can be refined.
DECISION
MAKING
CUSTOM
DEVELOPMENT
DEPLOYMENT &
TRAINING
Readiness
Assessment
Custom
Application
Development
Application
Development
Strategic
Planning
Prototype or
Proof of Concept
Business Case
Development
Data
Integration
Installation &
Customization
of Applications
Beta &
Pre-Release
Programs
Controlled
Pilots
Training
MANAGE
THE PROCESS
SERVICES
Business Case Development: Business cases help define a clear and purposeful solution based on well-defined
and documented business needs. Having a business case helps to justify good projects, stop bad projects
before they are started, and provides the basis for ongoing measurements after project completion to make
sure that the business is getting the results they wanted.
Operational Planning: In order to effect change on complex environments, it is necessary for organizations
to develop operational plans. These plans minimize the risks associated with large technology deployments.
Plans may incorporate key business processes and workflows, and help to identify any operational constraints.
Custom Development
Your organization requires solutions that meet you unique needs. CambridgeSoft consultants can assist with:
Custom Application Development: Assess business needs, document specifications, and create custom webbased solutions for your enterprise.
Data Integration: Create interfaces with other data management systems to incorporate your data into an
enterprise system.
Installation and Customization: Customize your solution to your specifications. Make certain that all technical and logistical installation processes are managed.
Deployment & Training
Develop a comprehensive road map for deployment of technology solutions across the enterprise. Our experts
help you plan and deploy your solutions by:
Application Deployment: Document, define and execute all of the actions required to support end user
acceptance. Manage the deployment process to assure a smooth roll-out to the end-users
Beta and Pre-Release Programs: Beta and pre-release programs involve a limited deployment to a small set
of users in order to identify deployment readiness or logistical issues that must be addressed prior to a largescale deployment. When early release programs are employed, the success rate of large scale deployments
is greatly increased and end users are more likely to adopt the new technology.
Controlled Pilots: Controlled pilots involve deploying a pre-production system to a small group of users to
evaluate it's functional, usability, technical, and operational characteristics in a real-world environment
prior to the completion of final system development. A controlled pilot helps identify and correct showstopper technology or operational issues before a final roll out program is implemented.
Training: Develop customized training materials for users, system administrators, and help desk personnel.
If you choose to outsource training management, CambridgeSoft can schedule and conduct training for
all users and stakeholders.
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Brackets
Chemical Symbols
Query Tools*
Table*
TLC Plate
Acyclic Chain
Templates
Cyclopropane
Cyclobutane
Cyclopentane
Cyclohexane
Cycloheptane
Cyclooctane
Scroll arrow
* = Pro or higher
MENUS
* = Pro or higher
= Ultra only
Apply a style to a
selected shape created with
the Pen tool.
Choose an open
document to display
as the active window.
Resize a selection.
Find Structure
Information and
Resources.
Browse Online
Resources.
13
Heres how
Duplicate a selection
CTRL+ALT+TAB
DRAWING TECHNIQUES
Draw a first bond
Move an atom
Draw a ring
Create a spiro-linkage
US
1 617 588-9300
FAX
1 617 5889390
WWW
EU
00 800 875 20000
FAX
+44 1223 464990
EMAIL
MAIL 100 CambridgePark Drive Cambridge, MA 02140 USA
IWE 05652 0304
www.cambridgesoft.com
info@cambridgesoft.com
ChemOfce.Com
CS ChemDraw
for Macintosh
Quick Reference
SCREEN ELEMENTS
Close box
Title bar
Window title
Menu bar
Rotation handle
Resize handle
Drawing area
Selection rectangle
Vertical scroll
bar
Document
window
Resize handle
Tools
palette
Text box
Scroll arrow
Horizontal scroll bar
Size box
TOOLS PALETTE
Ultra palette shown.
Varies with Pro & Std.
Lasso
Structure Perspective
Solid
Bond
Tools
Mass Fragmentation
Eraser
Multiple
Text
Dashed
Pen
Hashed
Arrows
Hashed Wedged
Bold
Bold Wedged
Hollow Wedged
Wavy
Ring
Tools
Marquee
Orbitals
Drawing Elements
Brackets
Chemical Symbols
Query Tools*
Table*
TLC Plate
Acyclic Chain
Templates
Cyclopropane
Cyclobutane
Cyclopentane
Cyclohexane
Cycloheptane
Cyclooctane
* = Pro or higher
MENUS
* = Pro or higher
= Ultra only
Shortcut Menu
The menu commands displayed depend on what
object you control-click in
the application. The following menu appears when you
control-click anywhere in a
document window.
Show/Hide Crosshair.
Show/Hide Rulers.
Minimize or expand document window.
Enlarge window.
Show/Hide Application Toolbars.
Rotate a selection.
Resize a selection.
Heres how
Duplicate a selection
E+
CTRL +
= command
= option
E = shift
DRAWING TECHNIQUES
Draw a first bond
Move an atom
Draw a ring
Create a spiro-linkage
US
1 617 588-9300
FAX
1 617 5889390
WWW
EU
00 800 875 20000
FAX
+44 1223 464990
EMAIL
MAIL 100 CambridgePark Drive Cambridge, MA 02140 USA
IME 05812 0304
www.cambridgesoft.com
info@cambridgesoft.com
ChemOfce.Com
CS ChemDraw
for Excel
for Windows
Quick Reference
SCREEN ELEMENTS
ChemDraw menu
Title bar
Excel toolbar
ChemDraw
toolbar
ChemDraw
structure
10
11
12
13 14
15
16
17
3. Export Table Export selected cells or the entire spreadsheet to an SDFile or ChemFinder database.
13. Filter Table Search for exact structures and substructures using the Search Query dialog box.
14. Similarity Table Search for similar structures using the
Similarity Query dialog box.
15. Show Picture Display molecules.
18
QUICK START
The following instructions are intended to give you a quick
start using CS ChemDraw for Excel. For more detailed
instructions, see the CS ChemDraw Users Guide.
CHEMDRAW MENU
The ChemDraw menu has all the same features as the tools
palette shown on the front of this card and more. See
reverse side for more complete descriptions.
To Start
1. From the Excel Tools menu, select Add-Ins. Be sure that
ChemDraw for Excel and Purchasing for Excel are checked.
2. Create a new ChemDraw/Excel worksheet by selecting
New ChemDraw Worksheet from the ChemDraw menu.
3. To convert an existing Excel worksheet to a
ChemDraw/Excel worksheet, select Convert/Update
Worksheet.
Entering Chemical Data
1. To draw a structure, double-click in any cell of a
ChemDraw/Excel worksheet. Insert your drawn
structure by closing the ChemDraw application or the
ChemDraw document window.
2. To import an open ChemFinder hit list, select Get
ChemFinder List from the ChemDraw menu.
3. To import an SD File or a ChemFinder database, select
Import Table from the ChemDraw menu and browse for
the file that you would like to import.
4. To convert a name to a structure, select a cell or cells with a
a chemical name in a ChemDraw/Excel worksheet and
select Convert Name to Molecule.
5. To convert a SMILES string to a structure, select a
cell or cells with a SMILES string in a ChemDraw/Excel
worksheet and select Convert SMILES to Molecule.
Name and Show Molecules
1. To name a molecule in a ChemDraw/Excel worksheet,
highlight the cell containing the molecule and select Name
Molecule.
2. ChemDraw structures in Excel are hidden by default,
showing only the name. To show the structure in a cell,
select the cell or cells, then select Show Picture.
Searching, Filtering and Sorting
1. To search a table by structure or substructure, select Filter
Table in the ChemDraw menu.
2. To search a table by structure similarity, select Similarity
Table in the ChemDraw menu.
Functions
1. To insert a function, select Function from the Insert menu
in Excel. Choose ChemDraw Functions from the Function
category list and then select a function you would like to
perform. Excel will then prompt you to click on the cell of
the molecule on which you want to perform the function.
US
1 617 588-9300
FAX
1 617 5889390
WWW
EU
00 800 875 20000
FAX
+44 1223 464990
EMAIL
MAIL 100 CambridgePark Drive Cambridge, MA 02140 USA
IWE 09214 0304
www.cambridgesoft.com
info@cambridgesoft.com
CS ChemOfce
Desktop to Enterprise Solutions
US
1 617 588-9300
FAX
1 617 5889390
WWW
EU
00 800 875 20000
FAX
+44 1223 464990
EMAIL
MAIL 100 CambridgePark Drive Cambridge, MA 02140 USA
www.cambridgesoft.com
info@cambridgesoft.com