Professional Documents
Culture Documents
Nmrmod - T - Copiar
Nmrmod - T - Copiar
Nmrmod - T - Copiar
Tutorial
Advanced Chemistry Development, Inc. Copyright 19942010 Advanced Chemistry Development, Inc. All rights reserved. ACD/Labs is a trademark of Advanced Chemistry Development, Inc. Microsoft and Windows are registered trademarks of Microsoft Corporation in the United States and/or other countries Copyright 2010 Microsoft Corporation. All rights reserved. IBM is a registered trademark of International Business Machines Corporation Copyright IBM Corporation 1994, 2010. All rights reserved. Adobe, Acrobat, PDF, Portable Document Formats, and associated data structures and operators are either registered trademarks or trademarks of Adobe Systems Incorporated in the United States and/or other countries Copyright 2010 Adobe Systems Incorporated. All rights reserved. Camtasia is a registered trademark of TechSmith Corporation, and Camtasia Studio is a trademark of TechSmith Corporation Copyright 19992010 TechSmith Corporation. All rights reserved. All the other trademarks mentioned within this reference manual are the property of their respective owners. All trademarks are acknowledged. Information in this document is subject to change without notice and is provided as is with no warranty. Advanced Chemistry Development, Inc., makes no warranty of any kind with regard to this material, including, but not limited to, the implied warranties of merchantability and fitness for a particular purpose. Advanced Chemistry Development, Inc., shall not be liable for errors contained herein or for any direct, indirect, special, incidental, or consequential damages in connection with the use of this material.
Table of Contents
Before You Begin ............................................................................................... v
About This Tutorial......................................................................................................... v
Advanced Understanding ......................................................................................................... v
1.
1.1 1.2 1.3 1.4 1.5 1.6
1.3.1
Manager or Processor.......................................................................................... 2 Changing Default Directories ............................................................................... 3 Quitting ACD/1D NMR Manager .......................................................................... 4
2.
2.1 2.2 2.3 2.4 2.5
3.
3.1 3.2
Processing Spectrum................................................................................ 9
Objectives ............................................................................................................ 9 Applying Interactive Fourier Transform .............................................................. 10
3.2.1 Defining Zero Filling ................................................................................................. 11 3.2.2 Applying Linear Prediction........................................................................................ 11 3.2.3 Specifying Window Function .................................................................................... 12 3.2.4 Correcting Phase...................................................................................................... 12 3.2.4.1 Automatically..................................................................................................... 13 3.2.4.2 Manually ............................................................................................................ 13
Obtaining the Power Spectrum .......................................................................... 14 Obtaining the Magnitude Spectrum.................................................................... 14 Removing Solvent .............................................................................................. 15 Dark Regions ..................................................................................................... 16 Correcting the Baseline...................................................................................... 17
Automated Baseline Correction ............................................................................... 18 Manual Baseline Correction ..................................................................................... 19
3.7.1 3.7.2
4.
4.1 4.2
Tutorial
Table of Contents
4.2.5
4.4.1 4.4.2 4.5.1 4.5.2 4.6.1 4.6.2 4.6.3 4.6.4 4.6.5 4.6.6 4.6.7
4.7
4.7.1 Specifying Peak Fitting Options ............................................................................... 38 4.7.2 Defining Region........................................................................................................ 39 4.7.3 Optimizing................................................................................................................. 40 4.7.4 Modifying Peak Parameters ..................................................................................... 41 4.7.4.1 Using the Mouse ............................................................................................... 42 4.7.4.2 Using the Dialog Box......................................................................................... 42 4.7.4.3 Batch Modification............................................................................................. 43
4.8 4.9
4.8.1
Defining Multiplets.............................................................................................. 46
4.9.1 Specifying Multiplets Analysis Options..................................................................... 46 4.9.2 Automatic Multiplet Building ..................................................................................... 47 4.9.3 J-Coupler .................................................................................................................. 48 4.9.3.1 Basic Multiplet Recognition ............................................................................... 48 4.9.3.2 Defining Multiplets Using J-Coupler.................................................................. 50 4.9.3.3 Setting Couplings Manually .............................................................................. 52 4.9.3.4 Adding Missing Peaks....................................................................................... 55 4.9.4 Connecting Multiplets Manually................................................................................ 58 4.9.5 Connecting Multiplets Automatically ........................................................................ 59
4.10
4.10.1 Verification................................................................................................................ 60 4.10.1.1 Dealing with Verification Results....................................................................... 64 4.10.2 Manual Assignment.................................................................................................. 66 4.10.2.1 Assigning by Peak............................................................................................. 66 4.10.2.2 Assigning by Multiplets...................................................................................... 67 4.10.3 Automatic Assignment.............................................................................................. 69 4.10.4 Comparing Manual and Automatic Assignments ..................................................... 70
4.11
4.11.1 4.11.2 4.11.3 4.11.4 4.11.5 4.11.6 4.11.7
Shortcut Mode................................................................................................. 71
Specifying Shortcut Mode Options........................................................................... 72 Action Helper ............................................................................................................ 73 Defining Dark Region ............................................................................................... 74 Setting Reference Point ........................................................................................... 75 Defining Multiplets .................................................................................................... 76 Assigning Multiplets.................................................................................................. 78 Quitting Shortcut Mode............................................................................................. 79
5.
5.1
Multispectral Operations......................................................................... 80
Objectives .......................................................................................................... 80
Tutorial
ii
Table of Contents
Loading Two Spectra ......................................................................................... 80 Synchronizing Spectra ....................................................................................... 81 Arithmetic: Adding and Subtracting Spectra ...................................................... 82 Working with Spectral Series ............................................................................. 83
5.5.1 What is a Series? ..................................................................................................... 83 5.5.2 Creating a Series...................................................................................................... 84 5.5.3 Creating a Series in Other Ways.............................................................................. 85 5.5.4 Coloring Spectra....................................................................................................... 86 5.5.4.1 Applying Auto Colors......................................................................................... 86 5.5.4.2 Applying System Color...................................................................................... 87 5.5.4.3 Applying Custom Colors.................................................................................... 88 5.5.5 Copying, Moving, and Deleting Spectra from a Series ............................................ 88 5.5.6 Processing Spectral Series ...................................................................................... 89
6.
Quanalyst ................................................................................................. 92
6.1.1 6.1.2 6.1.3 Objectives................................................................................................................. 92 Working with the Quanalyst dialog box .................................................................... 92 Adjusting the Quantitation Graph ............................................................................. 94
7.
7.1 7.2 7.3 7.4
7.5 7.6
8.
8.1 8.2 8.3
8.4 8.5
8.6
8.6.1 Specifying Plate Type............................................................................................. 114 8.6.2 Specifying a Group of Spectra ............................................................................... 115 8.6.3 Specifying Processing Options .............................................................................. 117 8.6.4 Attaching Structures to Spectra ............................................................................. 117 8.6.4.1 One by One..................................................................................................... 117 8.6.4.2 Group of MDL Molfiles .................................................................................... 118 8.6.4.3 Group from an SDfile ...................................................................................... 118
Tutorial
iii
Table of Contents
8.6.5
8.7
9.
9.1 9.2 9.3 9.4 9.5
Tutorial
iv
Advanced Understanding
This tutorial is intended to be a part of the technical documentation for ACD/Labs software. To study ACD/Labs products gradually, we recommend the following order of working through the technical documentation: 1. Documents for ACD/ChemSketch (CHEMSK_T.PDF), ACD/Dictionary (DICT.PDF), and ACD/3D Viewer (3D.PDF) to familiarize you with the features of drawing and looking up structures. 2. Reference manual (NMRMOD_R.PDF) and tutorial (the present document) for the ACD/1D NMR Processing Moduleto learn about the 1D NMR Module that is specific to the kind of ACD/SpecManager software you have purchased. If you have purchased the other modules of ACD/SpecManager, such as MS, UVIR, etc., the corresponding documentation is also supplied. In addition, it is advisable to have knowledge of the following ACD/Labs products: 1. ACD/SpecDB and ACD/SpecDB Enterprise (SPECDB_R.PDF and SPECDB_T.PDF) to learn about the Database window of ACD/SpecManager and Global Spectral Data Management System. 2. ACD/Forms Manager (FORMSMAN.PDF) is required to learn how to create input dialog boxes for user data and an interface for consistent database input. 3. ACD/Screen Editor (SCREDIT.PDF) will teach you how to create your own database screen form for a more convenient display of your data. All these documents you can find in the ACD/Labs documentation folder (\\DOCS).
Note
Tutorial
Mouse Conventions
You may perform several actions during your work with this software; the following specific words are used to describe them: Point to means move the mouse pointer to an item. Click or left-click means point to an item, and quickly press and release the left mouse button. Right-click means point to an item, and quickly press and release the right mouse button. Double-click means point to an item, and quickly press and release the left mouse button twice. Drag means point to an item, and press and hold down the left mouse button while you move the item. Select means highlight or make an interface element active by either clicking it or dragging over it (other actions are possible if specified in documentation). If used in "select the check box", it means that the check box should be marked with a tick (as opposed to "clear the check box" when the check box should be cleared, without a mark).
Operations
Many of the operations for processing and analyzing spectral documents within the Processor window can be performed by using various Operation Modes (e.g., Integration and Peak Picking) that can be accessed from the Operation toolbar. Note that when you enter any of these modes, the Operation toolbar is replaced with a new toolbar corresponding to the selected mode. The Operation toolbar for each mode includes two common buttonsAccept Changes Cancel Changes . To annul all of the changes made while working in the current mode and quit the mode, click Cancel Changes . be exited automatically and all of the changes will be saved as if you have clicked Accept Changes .
Important If you choose any command belonging to another mode, the current mode will
and
To keep all of the changes made in the current mode and quit the mode, click Accept Changes
Tutorial
vi
How to Contact Us
We are accessible through our Web site, phone, fax, and regular mail, but by far the most popular way to contact us is via electronic mail. Questions on pricing, sales, availability, and general issues should be directed to: info@acdlabs.com Technical and scientific support issues should be addressed by visiting: http://support.acdlabs.com Please tell us the name of the software purchaser; the product name, version number, build number, and license ID of the product you are contacting us about (from the Help menu, choose About to find this information); as well as a description of the problem you are having. If applicable, please tell us the name of the distributor from whom you purchased the software.
Online Updates
Updates of our Desktop and Enterprise products are made throughout the year. These intermediate releases (bringing the actual version number of a program, for example, from N.00 to N.01) often contain new functionality along with additional bug fixes and support for new file formats. To check if there is a new update available and to have this sent to you, please contact your local agent or our Technical Support Department. Before calling, we recommend that you have ready the name of the software purchaser, the product name, version number, build number, and license ID of the product you are contacting us about. All Desktop ACD/Labs software contains the capability to have software updates delivered online. You will need the registration numbers of the software and an Internet connection from the same computer on which the software is installed. For more information, refer to the ACD/Updater Users Guide located in the ACD/Labs documentation folder, \\DOCS\UP_CLNT.PDF.
Tutorial
vii
1. Program Basics
1.1 Objectives
This chapter will familiarize you with: Starting the program; Setting and changing file associations; Defining what version (Manager or Processor) you have or intend to use; Changing default directories for opening and saving files; and Quitting the program. Information about minimum system requirements as well as installation instructions are provided in the Quick Start Guide booklet which is included in every shipment of ACD/Labs software.
Tutorial
Program Basics
3. Choose what module you are going to use by selecting either the ACD/1D NMR Processor or ACD/1D NMR Manager options. To be able to complete exercises provided by this tutorial, select ACD/1D NMR Manager. If you have only 1D NMR Processor installed, this dialog box just informs you of that and you cannot use 1D NMR Manager. 4. Select the Use as Default check box to automatically enable the corresponding module as you start ACD/SpecManager. 5. Click OK to save changes.
Note
Tutorial
Program Basics
4. Click OK. 5. On the Window Switching bar, click ChemSketch ChemSketch window. to switch to the
6. From the Options menu, choose Preferences, and then, on the General tab of the dialog box that appears, specify the default directory for opening, saving, importing, and exporting files in the ChemSketch window:
In the Private box, you can set the directory for recording the configuration of the ChemSketch program (for example, TEMPLATE.CFG and GRSTYLES.STL files). 7. Click OK to close the dialog box, and then switch back to the Processor window by clicking Processor .
Note
Tutorial
Program Basics
Tutorial
Tutorial
Title bar Menu bar General toolbar Operation toolbar Macro toolbar
Note that the file name, the spectrum type, and the nucleus type are reflected in the status line along the bottom of the Processor window.
Tutorial
3. To have absolute correspondence with the images of the tutorial, specify the settings as displayed in the screen shot below. Otherwise, you may preserve the options that are to your taste.
4. Click OK to close the dialog box. Other tabs of the Preferences dialog box will be examined later in this tutorial.
Tutorial
The central part of the status bar (that is currently empty) can display different data depending on the option chosen in the Status Bar Settings dialog box: 1. From the Options menu, choose Status Bar to display the Status Bar Settings dialog box. 2. Make sure that the Spectrum Parameters option is selected and, in the adjacent box, from the drop-down list, choose Comment:
3. Click OK to place the data from the Comment line in the Parameters panel (if it is present there for the spectrum displayed) on the status bar:
4. To verify the spectrum origin and details, from the View menu, choose Spectrum Parameters. You will see the Parameters panel displayed.
Note
The spectrum Parameters cannot be modified within ACD/SpecManager. Good Laboratory Practice (GLP) requirements stipulate that parameters that are input at the time of recording the original data should not be changed by software which processes the data further.
correctly only if the AUDITA.TXT file is located in the same folder as FID.
Tutorial
3. Processing Spectrum
3.1 Objectives
This section of the tutorial provides you with the basics of spectrum processing. From a variety of handy features available in ACD/1D NMR Manager, we will examine the most up-to-date and easy-to use ones. You will learn how to: Use Interactive FT mode for: o o o o o Transforming FID into FT spectrum; Defining Zero Filling parameter; Applying linear prediction Specifying weighting function; Correcting phase.
Obtain power and magnitude spectra; Remove solvent; Set a dark region, and Correct the baseline.