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ACD/1D NMR Processor & Manager
Version 12.0 for Microsoft Windows
Tutorial
Processing and Organizing Experimental 1D NMR Data
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
Mouse Conventions ...................................................................................................... vi

Operations ................................................................................................................................vi
For More Information.................................................................................................vii

How to Contact Us ...................................................................................................................vii Online Updates ........................................................................................................................vii
1.
1.1 1.2 1.3 1.4 1.5 1.6
Program Basics ......................................................................................... 1

Objectives ............................................................................................................ 1 Starting ACD/1D NMR Manager .......................................................................... 1 Setting File Associations ...................................................................................... 1
Changing File Associations ........................................................................................ 2
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
Loading and Displaying Spectrum........................................................... 5

Objectives ............................................................................................................ 5 Loading Raw Data................................................................................................ 5 Elements of the Processor Window ..................................................................... 6 Changing Display Preferences............................................................................. 7 Displaying Spectral Data...................................................................................... 7
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
3.3 3.4 3.5 3.6 3.7
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
Analyzing Spectrum ................................................................................ 21

Objectives .......................................................................................................... 21 Labeling Peaks................................................................................................... 22
Automatic Peak Picking............................................................................................ 22 Manual Peak Picking................................................................................................ 23 Labeling an Arbitrary Position .................................................................................. 24 Changing the Appearance of Peak Labels............................................................... 25
4.2.1 4.2.2 4.2.3 4.2.4
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4.2.5
Deleting Peak Labels ............................................................................................... 26
4.3 4.4 4.5 4.6
Measuring Distance ........................................................................................... 26 Adjusting Spectrum to Reference Point ............................................................. 26

Automatic Detection ................................................................................................. 26 Manual Adjustment................................................................................................... 27 Inserting an Annotation ............................................................................................ 28 Deleting an Annotation ............................................................................................. 31 Manual Integration.................................................................................................... 31 Modifying Integral Curves......................................................................................... 33 Integration Options ................................................................................................... 34 Bucket Integration .................................................................................................... 35 Automatic Integration ............................................................................................... 36 Setting Reference Value .......................................................................................... 36 Changing Integral Appearance................................................................................. 37
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
Annotating .......................................................................................................... 28 Integrating Peaks ............................................................................................... 31
4.7
Peak Fitting ........................................................................................................ 37
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
Attaching Chemical Structure............................................................................. 44

Displaying a Structure in the Processor Window ..................................................... 45
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
Assigning Peaks and Verifying the Structure.................................................. 60
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
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5.2 5.3 5.4 5.5
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
Creating Report ....................................................................................... 97

Objectives .......................................................................................................... 97 Creating a Standard Report ............................................................................... 97 Report Page Setup............................................................................................. 99 Modifying the Spectrum Report........................................................................ 102
Changing the Spectrum Display............................................................................. 102 Changing the Table Display ................................................................................... 103 Changing the Structure Display.............................................................................. 103
7.4.1 7.4.2 7.4.3
7.5 7.6
Creating a Poster ............................................................................................. 104 Creating a Template-Based Report ................................................................. 105
8.
8.1 8.2 8.3
Macro Processing.................................................................................. 107

Objectives ........................................................................................................ 107 What Is a Macro and Group Macro? ................................................................ 107 Creating a Macro.............................................................................................. 107
Macro Organizer..................................................................................................... 107 Creating from Template.......................................................................................... 108 Creating Manually .................................................................................................. 108 Creating from History ............................................................................................. 110 Creating via Quanalyst ........................................................................................... 111 Settings for Macro Execution ................................................................................. 111
8.3.1 8.3.2 8.3.3 8.3.4 8.3.5 8.3.6
8.4 8.5
Editing a Macro ................................................................................................ 112 Managing Macros............................................................................................. 113

Placing Macros as Buttons on the Toolbar ............................................................ 113 Setting a Shortcut Key for Macro Execution .......................................................... 113 Autorunning a Macro upon Spectrum Loading....................................................... 114 Logging Macro Processing Results into a File ....................................................... 114
8.5.1 8.5.2 8.5.3 8.5.4
8.6
Processing a Group of Spectra (Group Macro)................................................ 114
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
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8.6.5
Executing Group Macro.......................................................................................... 120
8.7
Applying Intelligent Bucketing to Thousands of Spectra .................................. 122
9.
9.1 9.2 9.3 9.4 9.5
Integrating Experiment and Prediction................................................ 124

Objectives ........................................................................................................ 124 Preparing an Experimental Spectrum .............................................................. 124 Preparing Predictor Database.......................................................................... 125 Transferring Chemical Shifts............................................................................ 126 Using a Database to Calculate a Spectrum ..................................................... 128
Appendix. How To...................................................................................... 129

Objectives .................................................................................................................. 129 Register User Formats............................................................................................... 129 Import from an ASCII File .......................................................................................... 131 Shift FID Spectra........................................................................................................ 131 Apply Interactive Apodization..................................................................................... 132 Manipulate Windows.................................................................................................. 133 Enlarge Spectrum View ............................................................................................. 134 Lock a Display Range ................................................................................................ 135 Save Spectral Region as an Individual Spectrum...................................................... 135 Edit a Spectrum ......................................................................................................... 135 Update Spectrum User Data via Data Form .............................................................. 136 Update Structure User Data via Data Form ............................................................... 136 Select a View Mode for Selected Spectra.................................................................. 137 Search in Databases. General Notes ....................................................................... 137 Search Shifts in NMR Predictor Databases ............................................................... 138 Perform Peak, Mixture, Multiplet, and Similarity Searches ....................................... 139 Apply Direct Assignment............................................................................................ 139 Update Structure with Assignment............................................................................. 140 Link Documents ......................................................................................................... 140 Customize Panels Display in the Processor Window ................................................ 141 Manipulate Tables...................................................................................................... 142
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Before You Begin

Thank you for purchasing 1D NMR module of ACD/SpecManager, ACD/1D NMR Manager. We have endeavored to produce the easiest to use, most powerful data processing and spectral data management system for various types of spectroscopic and chromatographic data.
About This Tutorial

Completion of this tutorial should have given you the tools needed to get started with the 1D NMR module of SpecManager, it is designed for either online use or to be printed and used as a hard copy version. The screen shots shown throughout this reference manual have been taken with a relatively small window size. The colors and other properties of the window elements described throughout this manual correspond to the Windows Classic Theme (with dismissed gradients) of the operating systems Display Properties. This tutorial is provided in electronic form, readable with Adobe Acrobat software. If you cannot locate an index topic you need, please do a text string search for the relevant word or phrase, or related words.
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
Before You Begin
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
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Before You Begin
For More Information

To see the latest in ACD/Labs software and services, please visit our Web site at http://www.acdlabs.com/ Our Web site is being accessed at the rate of tens of thousands of hits per day. Theres a reason for this: much is offered through our Web site. We offer free ChemSketch, an ACD/LogP Freeware Add-on for ChemSketch, a free ISIS 3D Add-in, free ChemDraw extensions, and a free 2-week demo key for Interactive Laboratory sessions where you can run test calculations using Java applets without purchasing software. There are TechSmith Camtasia-based movies available for download which show the operation of many of our software packages (especially ChemSketch). We are constantly updating the information on our Web site. The Web site will tell you at which scientific conferences you can visit the ACD/Labs booth. You can browse the Frequently Asked Questions page or drop in and chat on our newsgroup, which can also be reached via our Web site. If you would like to stay informed of the latest developments in chemical software at ACD/Labs, please be sure to sign up for e-mail broadcasts at our Web page: http://www.acdlabs.com/feedback/mailing.html If you would like to participate in the ACD/Labs forums, please access: http://forum.acdlabs.com/
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.
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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.
1.2 Starting ACD/1D NMR Manager

Once ACD/SpecManager, ACD/NMR Processor, or ACD/1D NMR Manager has been installed on your computer, follow these basic steps to start it: 1. Start Microsoft Windows. 2. On the Windows desktop, double-click ACD/SpecManager icon. OR On the Start/Run menu in the Windows taskbar, point to ACD/Labs, and then choose the ACD/SpecManager icon. OR In the folder where you have installed all ACD/Labs software, double-click the program file SPECMAN.EXE. OR If you have other ACD/Labs programs running, from the ACD/Labs menu, choose SpecManager. 3. As a result, you should see the splash screen, and then the empty Processor window is activated. Now you are ready to import or open a spectrum.
1.3 Setting File Associations

If this is the first time you have started the program, the File Associations dialog box appears. This contains a selectable list of file extensions and file types, which you may set to open automatically with ACD/Labs software from now on, whenever a file of that type is double-clicked. If so, select the check boxes of the file formats you want to add, and then click Yes. If you do not want ACD/SpecManager to automatically open files with the listed extension, or are not sure, leave the check boxes blank and click No. Note If you displayed the File Associations dialog box (from the File menu, choose File Associations) under Windows NT but have no rights to change file associations, a warning message appears. Contact your system administrator to resolve this matter.
Tutorial
Program Basics
1.3.1 Changing File Associations

If you have not selected all formats, the default file association can be viewed or changed at any timefrom the File menu, choose File Associations. If all ACD/Labs supported file extensions have already been associated, then you will receive a message, all supported file types are already associated with the current application. In this case, you can change the file associations through Windows Explorer. 1. Open Windows Explorer. 2. Right-click the file with the extension for which you want to create the association. 3. From the local menu that appears, choose Open With. 4. Set the application that should be used to open the file, and then select the Always use this program check box. 5. Click OK and close Windows Explorer.
1.4 Manager or Processor

To check what module1D NMR Manager or 1D NMR Processor (without the SpecDB module and Database menu commands)you have installed and/or to specify the module you want to work with, you can use the Select Module dialog box. 1. When no files are open in the Processor window, from the Options menu, choose Modules. 2. In the dialog box that appears, from the Type list, select 1D NMR:
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
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Program Basics
1.5 Changing Default Directories

If you are running a single-user (stand-alone) copy of ACD/1D NMR Manager, the default directory settings are likely fine. If you have a network copy of ACD/1D NMR Manager, it is advisable to change the default directory settings in the ACD/Labs software so that the default drive for saving work-in-progress is the users local hard drive, not the remote server. After creating local access for either limited or unlimited numbers of seats, follow the below steps at each local installation: 1. From the Options menu, choose Default Directories. 2. In the Default Directories dialog box that appears, make sure that 1D NMR tab is active. 3. In the corresponding boxes, specify the directories that will be opened by default while opening, saving, importing, or exporting files as well as opening or saving macros in the Processor window:
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
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Program Basics
1.6 Quitting ACD/1D NMR Manager

Information provided in this section is intended to familiarize you with possible ways of quitting ACD/1D NMR Manager. To continue with this tutorial, do not quit ACD/1D NMR Manager. You can quit from the program in any of the following ways: . 1. On the title bar of any window, click Close 2. From the ACD/Labs menu, choose Exit All. This will attempt to quit all of the ACD/Labs programs that are currently running, one after another. 3. From the File menu, choose Exit. This will close only the ACD/Labs program you are working with at the moment. You will be prompted to save your work.
Tutorial
2. Loading and Displaying Spectrum

2.1 Objectives
In this chapter, you will learn how to: Load a spectrum file into the 1D NMR module; Determine information about the spectrum (type, units, and filename) at a glance; and Change display preferences.
2.2 Loading Raw Data

To demonstrate the abilities of 1D NMR Manager, we will use the HNMR spectrum of catechin (look for FID file in the EXAMPLES\SPECMAN\1DNMR\CATECHIN.FID folder). 1. On the File menu, point to Import, and then choose From 1D NMR Directory or click Open/Import Spectrum to display the Import dialog box. 2. Select a file format of (Auto Detect) and click drives and directories until you are in the EXAMPLES folder provided with your software which contains the file FID in the \CATECHIN.FID directory. (The path name is likely C:\ACD12\EXAMPLES\SPECMAN\1DNMR but if you are having trouble finding it, use your system finder.) 3. Click Open and the file will be loaded.
Tutorial
Loading and Displaying Spectrum
2.3 Elements of the Processor Window

When describing the program throughout this tutorial, some terms defining various parts of its interface are used. Below you will find the picture showing the interface arrangement:
Title bar Menu bar General toolbar Operation toolbar Macro toolbar
Spectrum Display area
Scales Status bar Window Switching bar
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
2.4 Changing Display Preferences

The multi-tab Preferences dialog box allows you to specify the way all of the spectra loaded into the Processor window should be displayed. 1. From the Options menu, choose Preferences. 2. Practice changing the display by varying the set of options and clicking Apply .
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.
2.5 Displaying Spectral Data

The status bar located at the bottom of the Spectrum Display area providing the required information on the document you are working with. On the left-hand side of the status bar, you can see the name of the current spectral file and the active mode (FID or it may be Apodization, Peak Picking, etc.). On the right-hand side of the status bar, there are buttons for switching between the units of measurement for the X-axis and between the Normalized and Absolute Intensity view modes (for series):
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.
5. For later use, note that the compound is catechin.

Tip For the TOPSPIN format, ACD/SpecManager will read the time of data creation
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.
This chapter covers material that partially appears in the movie 1dnmr_1.exe which can
be downloaded from our Web site. Also, by default, it is placed in the MOVIES folder at the time of installing ACD/1D NMR Manager.
Tutorial
Processing Spectrum
3.2 Applying Interactive Fourier Transform

The program allows you to interactively and quickly adjust the most suitable parameters for the Fourier transformation and spectrum phasing. 1. On the Operation toolbar, click Interactive Fourier Transform integrated Fourier Transform dialog box appears in the compact form: . The
Important This dialog box allows you to reprocess FT-ed spectra without loosing any
specified data (peak labels, assignment, etc.) at any stage of analysis. Note that the default settings are specified and the Apply FT and Instant Preview check boxes are selected. to apply Fourier transform using the default settings and display 2. Click Preview the result without closing the dialog box:
Tip To convert the FT spectrum back to the corresponding FID, just clear the Apply FT
check box.
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Processing Spectrum
3. If the obtained spectrum suits your requirements, click OK in the Fourier Transform dialog box and proceed with Section 3.3. In our example, to demonstrate all the power of Interactive FT and familiarize you with the options available in the dialog box, we will slightly modify the obtained spectrum.
3.2.1 Defining Zero Filling

To enhance spectrum resolution, let us specify Zero Filling settings first. 1. Keep the value of the Initial box (number of data points recorded during the signal detection period) unchanged. 2. In the Final box, insert 32768 by clicking arrows on the right to set the number of points that will be used by Fourier Transform:
In our example, there is no need to shift FID, so we will proceed directly with linear prediction. For the information on how to specify settings for shifting FID spectra, refer to Appendix. How To
3.2.2 Applying Linear Prediction

Linear prediction allows you to remove artifacts or distortion, caused by delayed acquisition or problems with the initial points of a FID and improve resolution in 1D NMR spectra with a short time domain. Backwardis used to correct the first few corrupted data points in the FID. Note that the default value for the number of points to back predict is 1 and should usually be a small number. The default value for the number of base points is set corresponding to the Initial Size value. The optimal number of LP coefficients (Coeff. Count) should not exceed 1/4 to 1/3 of common quantity base points. Forwardis used to improve resolution in cases where the FID is badly truncated. This is usually not the case for routine 1D NMR spectra, so forward linear prediction is not generally recommended. Note that the number of LP coefficients used for forward prediction should be slightly greater than the number of expected peaks in a spectrum. 1. In the Fourier Transform dialog box, click Linear Prediction .
2. In the area with options for linear prediction that appears, select the Backward check box and specify the values as shown in the picture below:
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Processing Spectrum
The linear prediction is automatically applied to the spectrum in accordance with the settings we have specified. Tip Alternatively, you can apply linear prediction to a FID by clicking Linear Prediction on the Operation or Apodization toolbar and specifying the required options in the dialog box that appears. For convenience purposes, after the required settings are specified, you can hide the Linear Prediction (or any other) area of the dialog box by clicking the corresponding button.
3.2.3 Specifying Window Function

It is recommended to multiply the spectrum by a weighting function (especially for 13C spectra). A weight functionalso called a window functionis normally used to reduce noise in the spectrum. 1. Click Window Function type of apodization to be applied. to display the area where you can choose the
2. For the given example, we recommend that you select the User type of apodization, and then choose EM (exponential multiplication function). 3. In the corresponding line-broadening box (LB column), specify the value 0.2.
If required, the pulse-delay time can also be set in the Time box of the Tm (sec) column. Note that the spectrum is modified somewhat.
Note
3.2.4 Correcting Phase

Now we can correct the phase of the obtained FT spectrum. The phase can be corrected in two ways: automatically or manually. Press PAGE UP several times to vertically zoom in the bottom part of the spectrum.
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Processing Spectrum
3.2.4.1 Automatically
There are three algorithms for automated phase correction: simple, correction by optimizing the baseline, or correction by symmetrizing the spectrum lines. The second method is highly efficient for 1H-spectra. The third one is more useful for 13C-spectra. 1. In the Fourier Transform dialog box, click Auto Simple spectrum changes a little. . You should see the
Tip To keep the value of the first order phase parameter (Ph1) untouched during the Auto
Phasing Simple or Auto Phasing by Baseline Optimization procedures, click Phasing Parameters box. , and in the area that appears, select the Fix check or
2. Try other methods of phase correction by clicking Auto BL Opt Auto Symm (If required).
3.2.4.2 Manually
If you wish to refine the result, you can correct the phase manually. This operation will involve the use of both the left and right mouse buttons. These are shortcuts to the phase buttons in the Phasing Parameters area:
1. In the Fourier Transform dialog box, click Mouse Phasing . You will see the colored vertical line that defines the phase pivot point, which automatically is set to the highest peak in the spectrum. 2. To change the zero order phase (Ph0) only, drag over the peaks with the left mouse button. 3. To adjust both the Ph0 and Ph1 parameters so that the peak marked with the red line remains, drag with the right mouse button. You can drag the red line to place it over another peak.
Tip You can also specify both parameters either by entering the values manually or by
clicking the arrows to the right of the corresponding field in the Phasing Parameters area. 4. If you are not satisfied with the obtained result, in the Fourier Transform dialog box, click Fine Tuning . Unlike Mouse Phasing, this mode allows you to adjust the phase in most accurate way (in increments from 1 to 5). 5. Drag with the left mouse button to control the first phase parameter (Ph0). Drag with the right mouse button to change the second phase parameter (Ph1). 6. As soon as you obtained the desired spectrum, click OK to quit the Interactive FT mode and close the Fourier Transform dialog box.
Note
If you are not satisfied with the results of spectrum processing, try other settings until the required spectrum is obtained. .
7. Zoom out to the whole spectrum by clicking Show Whole Spectrum
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3.3 Obtaining the Power Spectrum

1. With the Fourier transformed spectrum displayed, from the Process menu, choose Power Spectrum. Since this operation has the effect of squaring each y-value, the relative intensity of lines changes considerably. Note that some of the processing options become unavailable. 2. Click Rectangular Zoom and drag over the peaks to observe them:
3. Zoom out on the spectrum by clicking and to go back to the usual spectrum view by clicking the Process menu, and then Power Spectrum again.
3.4 Obtaining the Magnitude Spectrum

1. To convert a transformed spectrum with real and imaginary output to a magnitude spectrum, from the Process menu, choose Magnitude Spectrum. Zoom in the spectrum part using the Rectangular Zoom tool (
).
2. Similar to the Power Spectrum mode, the Magnitude Spectrum mode disables some of the processing options. ) and go back to the usual 3. Zoom out the spectrum (click Show Whole Spectrum spectrum view by choosing Magnitude Spectrum from the Process menu again.
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3.5 Removing Solvent

This option allows you to remove unnecessary spectrum signalse.g., solvent signals. 1. From the Process menu, choose Remove Solvent Signal to enter the new mode and display a new toolbar. Note that the red lines are set over the spectrum. If the solvent signal is specified in the Spectrum Parameters of the current spectrum, the solvent signal is automatically defined. If the program cannot find the solvent, the region in the center of the spectral curve is selected. to display the Remove Solvent Options dialog 2. Click Remove Solvent Options box. In this dialog box, select Frequency Domain Filter, and then click OK:
3. To select a region to be removed, point to the red lines and drag them so that the central line defines the center of the solvent signal and two other linesits width. Or you may also use the input boxes on the toolbar to specify the position of the region and its width:
In this case, we should remove the signal of water that is always present in DMSO as an admixture, so the recommended values for the region to be removed in the current example are Solvent Position = 3.38 ppm and Frequency Domain Filter Zone Width = 70 Hz. You can also use the Remove Solvent Options dialog box (see point 2) to specify the solvent region and the type of filter that should be used. 4. Once the region is defined, on the Remove Solvent Signal toolbar, click Remove Solvent Signal .
Note
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After some processing time, you will see the spectrum change considerablythe solvent signal has been removed and the curve is modified accordingly:
If you find the results inappropriate, click Clear to cancel any changes made in the mode and try another method. 5. In the next section, we are going to remove the same solvent signal by defining it as a dark region. To exit this mode without saving the changes, click Cancel Operation .
Note
3.6 Dark Regions

In Section 3.5, we have learned to remove unnecessary spectrum signals by using the Remove Solvent Signal command. Now, let us try to get the same result by setting the dark region. 1. From the Analysis menu, choose Dark Regions. to display the 2. In the Dark Region Organizer dialog box that appears, click Edit Edit Dark Region dialog box. For more information on the dialog box, refer to the ACD/1D NMR Processor and Manager Reference Manual (NMRMOD_R.PDF) located in the ACD/Labs documentation folder (\\DOCS). 3. In the Description field, type HDO to define the annotation. 4. In the From (ppm) and To (ppm) boxes enter 3.3 and 3.4485 correspondingly, as shown in the picture below. 5. Select the Active check box (otherwise, the dark region will be added to the Dark Region Organizer dialog box but will not appear on the spectrum); the Apply to the Calculated Spectrum check box should remain clear.
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6. Click OK to return to the Dark Region Organizer dialog box. Note that the dark region is added to the list of dark regions. 7. Click OK to close the Dark Region Organizer dialog box. Note that the dark region is now defined on the spectrum.
Dark Region
To change the color of the dark region, from the Options menu, choose Preferences. On the Spectrum tab that is displayed, click the Dark Region color box to display the color palette, and then select the appropriate color. All information on dark regions is stored in the Dark Region Organizer dialog box.
Note
Using the buttons to the right of the list in the Dark Region Organizer dialog box, you can add, edit, delete dark regions, and also search for a solvent you want to appear as a dark region (the Solvents button). The Solvent Shifts dialog box contains solvents referring to an active spectrum nucleus alongside their chemical shifts making the definition of the applied solvent fast and easy. Tip To manipulate a specified dark region when in the Shortcut or Peak Picking mode, just click it, and choose the required command from the shortcut menu.
3.7 Correcting the Baseline

On the Operation toolbar, click Baseline Correction . This will cause a new Baseline Correction toolbar to appear. You can correct the baseline in two ways: by using one of the automatic methods or by adjusting some of the baseline points manually.
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3.7.1 Automated Baseline Correction

1. First, let us specify the methods and other parameters for automatic correction. Click Baseline Correction Options to display the Baseline Correction Options dialog box. In this section, we place emphasis on the lower part of the dialog box containing settings for automatic correction:
2. For the current example, we recommend that you choose the Spectrum Averaging method and set the Box Half Width parameter to 15 and Noise Factor to 1. 3. Click OK in the dialog box to apply the changes. 4. For a better view of the baseline, let us zoom in the lower part of the spectrum. Press PAGE UP several consecutive times to enlarge the lower part of the spectrum:
5. As you can see, the spectrum baseline is somewhat distorted. We will try to correct it. Click Auto Detect Baseline . The red line fits the spectrum baseline:
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6. To view the resultant spectrum, click Show Result
7. Zoom out to the whole spectrum by clicking Show Whole Spectrum
3.7.2 Manual Baseline Correction

Sometimes, automatic baseline correction is not enough and some manual adjustment is required. 1. While in the Baseline Correction mode, drag over the spectrum region you are going to adjust. For example, define the region from about 8.7 to 9.3 ppm:
2. Click Rectangular Zoom (or hold down CTRL and right-click in the workspace to enable this tool) and drag over the spectrum region to enlarge it:
3. On the Baseline toolbar, click Add/Move Baseline Points correction mode.
to enable the manual
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4. Point with the special cursor to the place where you want to set the baseline node, and then click. Repeat this step until the baseline of the required form is constructed. Note that the baseline will only be modified within the set limits:
Tip If you have accidentally placed the wrong node, you can remove it. On the Baseline
Correction toolbar, click Delete Baseline Points selector over the node(s) you want to remove.
and drag a rectangular
5. To view the spectrum with the resultant baseline, click Show Result
6. Zoom out to display the whole spectrum ( current baseline and quit this mode.
). Click Accept Changes
to save the
7. Save the processed spectrum into a separate file. From the File menu, choose Save As and specify a new name for it, for example, CATEC_FT.ESP. Note that we are going to use this file in the subsequent chapters.
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4. Analyzing Spectrum
4.1 Objectives
A spectroscopist needs to communicate the information deduced from a spectrum to the next person who views the spectrum. One of the most efficient means to do this is by directly designating this information on the spectrum. In this chapter, you will learn how to: Label peaks using automatic and manual methods; Measure the distance between peaks; Adjust the spectrum to a reference point; Insert appropriate annotation for peaks or regions of the spectrum, Automatically or manually integrate peaks; Optimize the peak curve using Peak Fitting; Attach a structure to the spectrum; Define multiplets and coupling constants automatically and manually; and Assign portions of the structure to the spectrum and verify the spectrum against the structure.
This chapter covers material that appears, in part, in the movie 1dnmr_2.exe which can
be downloaded from our Web site. Also, by default it is placed in the MOVIES folder at the time of installing ACD/1D NMR Manager. For this chapter, we recommend that you open the CATEC_FT.ESP file that was saved in the previous chapter. Close all the spectra currently open in the Processor window, load CATEC_FT.ESP, and proceed with the following steps. You can also use the CATECHIN.ESP file from the EXAMPLES folder. To follow the exercises described below, on the Edit menu, point to Clear, and then choose All Tables to clear all of the labels in the CATECHIN.ESP file. Note Depending on the spectral file you will use to perform the following exercises, data shown in various tables and pictures throughout this chapter of the tutorial may slightly differ from those you can see on your screen.
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4.2 Labeling Peaks

You can label peaks in the spectrum in several ways: using the auto peak picking mode, manual peak level, or peak-by-peak mode. We will demonstrate all the methods. 1. If a part of the spectrum is currently enlarged, on the General toolbar, click Show Whole Spectrum .
and select the area of the spectrum 2. On the General toolbar, click Horizontal Zoom containing all of the signals (from about 1.5 to 9.5 ppm) by dragging. 3. On the Operation toolbar, click Peak Picking toolbar appears. . Note that a new Peak Picking
4.2.1 Automatic Peak Picking

1. On the Peak Picking toolbar, click Auto Peak Picking . Labels will be placed on all of the peaks in accordance with the default parameters (noise factor, minimum height) set in the Peak Picking Options dialog box. 2. To change the default parameters, on the Peak Picking toolbar, click Peak Picking Options to display the Peak Picking Options dialog box.
3. Specify the required Noise Factor and Minimum Height (peaks smaller than the specified height barrier are not labeled) or Minimum S/N (peaks whose height to RMS Noise ratio is smaller than the specified value are not labeled) either by clicking the arrows to the right of the corresponding fields or by entering the values manually. Click OK.
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4. Click Remove All Labels in Zoom Area
to clear the labels that were inserted in on the
accordance with the previous parameters, and then click Auto Peak Picking Peak Picking toolbar again to insert labels with the newly set parameters:
4.2.2 Manual Peak Picking

Before proceeding to the next step, click Remove All Labels in Zoom Area the labels set in the previous section. to remove
and move the 1. On the Peak Picking toolbar, choose Select Peak Picking Level mouse over the workspace. Note that the horizontal red line appears in the Processor window and is attached to the mouse pointer. 2. Move the mouse to specify the minimum peak height and click to fix it. Note that the labels appear on all of the peaks higher than the selected level with no regard for the default minimum peak height.
3. On the Peak Picking toolbar, click Adjust Peak insert a label for the selected peak.
. Now you can remove or
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4. To insert a label, move the mouse pointer to any unlabeled peak and click when it is highlighted. Note that the label appears.
5. To remove a label, move the mouse pointer to any labeled peak and click when it is highlighted.
4.2.3 Labeling an Arbitrary Position

If you want to mark a chemical shift between doublets or quartets, on the shoulder of a larger peak, or at any position where the point of a peak does not occur, this command is especially helpful. ), 1. In the Manual Peak Picking mode with the Adjust Peak button pressed in ( while holding down SHIFT, click where you want to locate the peak. A label will appear. For example, here is peak picking for the center of a quartet:
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2. For the current example, remove the current peak label from the center of a quartet. Move the mouse pointer to it while holding down SHIFT, and click when it is highlighted.
Tip To make it easy to insert/remove peak labels, use Rectangular Zoom
to enlarge
the required spectrum region. 3. Click Accept Changes

Note
to save the labels and quit the Peak Picking mode.
All of the described commands are applied to the selected fragment of the spectrum only.
4.2.4 Changing the Appearance of Peak Labels

1. From the Options menu, choose Preferences, and then switch to the Labels tab:
2. If necessary, change the color, size, and font used for labels. Note that these settings will also be applied to other labels: annotations, assignments, and multiplets (see the chapters later in this guide). 3. Now switch to the Peaks tab:
4. If required, change positions and orientation of the labels, as well as the decimal accuracy of values. To check if the changes made are appropriate without closing the dialog box, click Apply. To accept the changes and close the dialog box, click OK.
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4.2.5 Deleting Peak Labels

1. On the General toolbar, click Show Table of Peaks to display the Table of Peaks.
2. In the Table of Peaks, highlight the line containing the reference name. 3. Press DELETE or right-click that line and, from the shortcut menu, choose Delete Label. The peak label will disappear from the displayed spectrum.
4.3 Measuring Distance

You can measure distance between any two points of the curve using Measure Distance: Point to Point or exactly between two peaks using Measure Distance: Peak to Peak to zoom out. . .
1. Click Show Whole Spectrum
2. On the General toolbar, click Measure Distance: Peak to Peak
3. Point to the required peak, and then click to fix the first blue line. Then click any other peak to set the second line. You can see the coordinates of the marked peaks and the distance between them on the status bar. Note that the distance is always displayed in Hz regardless of the currently selected unit:
4. Disable the tool by clicking the button again.
4.4 Adjusting Spectrum to Reference Point

On the Operation toolbar, click Reference Spectrum toolbar. to display a new Reference
4.4.1 Automatic Detection

For 13C and 1H spectra ACD/SpecManager includes the automatic reference peak detection feature. 1. First, we are going to set the preferences. On the Reference toolbar, click Reference Options to display the following dialog box:
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2. Note that the solvent defined in the Parameters panel of the spectrum is automatically displayed in the Solvent box. In this case it is DMSO-d6. If necessary, you may set another solvent, though, for our example, it is recommended to set options as displayed in the above picture and click OK.
Note
If the spectrum contains both TMS and solvent signals, the TMS peak is only used for scale adjustment.
3. On the Reference toolbar, click Auto Reference . Based on the data in the Parameters panel of the current spectrum, this feature automatically determines the possible reference peak, adjusts the spectrum according to it, and annotates the peak (notice the DMSO-d6 annotation for the peak at about 2.5 ppm):
4.4.2 Manual Adjustment

In case the program cannot find a solvent or TMS peak automatically, you can define the reference peak manually. 1. Click Clear Changes to cancel changes made by the Auto Reference feature.
2. Move the mouse pointer to the peak to be referenced, in this case, DMSO-d6, and click when it is highlighted. (This is the small peak around 2.48). Note that when moving the pointer over the reference peak, you should hold it above the X-axis for the highlight to show.
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3. In the Solvent Shifts dialog box, select DMSO-d62.50 from the list. As you can see, this dialog box contains a list of standard reference points for the active spectrum nucleus with annotations. If you want the annotation to be attached to the peak, select the Add Annotation check box.
Tip You may also add new entries or edit the list of standard reference points using the
group of boxes and buttons at the bottom of the dialog box. To restore the default table, click Restore. 4. Click OK. Note that all of the shifts are recalculated relative to the specified reference point. 5. Click Accept Changes
Note
to save the changes and quit this mode. and the annotation (if you have selected the latter) from the .
To delete a Reference peak designation, you should delete both the peak from the Table of Peaks
Table of Annotations
4.5 Annotating
In the Annotation mode, you can annotate either a single peak or a spectral region and assign annotations to ten different layers.
4.5.1 Inserting an Annotation

We will demonstrate the region annotation: 1. On the Operation toolbar, click Annotate Peak/Region .
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2. On the Annotation toolbar, click Options dialog box.
to display the Layer Label Options
3. In this dialog box, specify the required options for the labels of different annotation layers and information that is to be inserted into them. For the current example, select the second layer and set options as displayed in the picture below:
According to the specified settings, all the annotation labels of the second layer will include the date of creation, layer number, and fields for displaying the updating date and name of a person who will perform this. 4. Drag over the leftmost peaks in the spectrum to select the area to be annotated.
Note
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5. As you release the mouse button, the Edit Annotation dialog box appears where you can enter the desired annotation and specify a layer for it.
To add the annotation as a dark region, select the Add as Dark Region check box. For more information, refer to Section 3.6. 6. Click OK to attach the annotation to the specified region (make sure that the button corresponding to the current layer is active on the Annotation toolbar( )):
Note
Tip To apply the annotation to a single peak, just click it with the Annotation mode active.
7. To temporary hide the annotation, on the Annotation toolbar, click to the layer number) to cancel its selection:
(button corresponding
8. Click Accept Changes

Note
to save the changes and quit this mode. To display the whole .
spectrum, on the General toolbar, click Show Whole Spectrum
If you then decide to edit the annotation, click it with the Annotation mode active and make changes to the dialog box that appears.
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4.5.2 Deleting an Annotation

1. To delete an annotation, open the Table of Annotations by clicking on Show Table of Annotations . 2. In the table, highlight the line containing the name of the reference. 3. Press DELETE. OR Right-click that line and from the shortcut menu that appears, choose Delete Annotation. The text annotation will disappear from the displayed spectrum.
4.6 Integrating Peaks

There are two ways to integrate peaks: by the automatic integration of the whole spectrum or by manual integration of the selected spectrum segments. We will demonstrate both ways. On the Operation toolbar, click Integration appears. . Note that a new Integration toolbar
4.6.1 Manual Integration

We will start with the manual integration procedure. 1. If necessary, zoom in to the region you want to integrate. 2. On the Integration toolbar, click Select Segments for Integration area of the spectrum you want to integrate by dragging over it. and select the
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3. You can also integrate the entire curve first and then divide the integral curve into smaller parts. To do that, drag over the entire spectrum to place an integral curve:
4. Select any part of this integral curve by dragging over it. Repeat this step as many times as you need until all the necessary portions are integrated.
5. Click Select Segments for Integration
to exit the Manual Integration mode. on
6. Remove superfluous integral curves. Select the integral curve segment or the integral curve you want to remove by clicking it, and then click Delete Selected Integral Curves the Integration toolbar:
Note
To display the Table of Integrals, on the General toolbar, click Show Table of Integrals or, from the View menu, choose Table of Integrals.
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4.6.2 Modifying Integral Curves

You can move the created integral curves vertically and resize them in both horizontal and vertical directions. 1. Select any integral curve by clicking on it. 2. Zoom in to any peak for which the integral has been calculated. Place the mouse pointer over the top or bottom side of the rectangular selector of the integral curve so that the arrows appear instead of the cursor and drag it vertically. Note that all of the other integrals are resized with the selected one. The blown-up portion of the peak around 3.8 ppm will look approximately like the following:
Tip To deselect the integral curve(s), click outside the rectangular selection. 3. Place the mouse pointer at the center of the rectangular selection of the integral curve and drag it vertically. Note that you can only move the selected integral curve. You can move every integral curve in a similar manner:
Note
To move all or several integral curves at a time, select them either by dragging a selection box around them or by clicking them while holding down SHIFT, and then move the rectangular selection.
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4. Place the mouse pointer over the left/right side of the rectangular selection that surrounds the integral curve so that the arrows appear instead of the cursor and drag it horizontally to expand or narrow the integration area:
5. Click Show Whole Spectrum
to return to the whole spectrum view.
4.6.3 Integration Options

Before starting automatic integration, we are going to set the integration options and reference. to display the Integration 1. On the Integration toolbar, click Integral Options Options dialog box. You can choose among two types of automated integration:
2. If you set the option as displayed above (with the Detect Signal Intervals check box selected) the segments of the spectrum that contain signals will be integrated only. The integrals in this case will be plotted as separate segments. If this check box is cleared, the solid integral curve will be plotted for the whole spectrum. The Noise Factor is the parameter (%) that defines the spectrum signal. If the resultant integral has a value smaller than 1/1000th of the maximum integral, it is deleted. The remaining regions calculated in such a way are combined if they are 5 Hz apart. 3. At the bottom area of the dialog box, specify the reference value:
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To normalize integrals to your internal standards, select the Internal Standard option and define the custom integral region and value in the Range and Value boxes correspondingly.
4.6.4 Bucket Integration

The middle segment of the dialog box for integration options represents a Bucket Integration feature that is primarily of interest to studies in the field of metabonomics. 1. If you choose this option, the spectrum will be split into equal-width portions which will be integrated. You can either set the number of portions (Number of Buckets value) or the width of each portion (Width of Bucket value). When the Group Treatment mode is on, Bucket Integration applied to the currently active series will create buckets with the same starting and final points for all the spectra.
Note
The position of every bucket can be manually adjusted in the Group Treatment mode. If you are working with a series of spectra, selecting the Intelligent Bucketing option will calculate the temporary spectrum to which Bucket Integration will be applied (for a single spectrum, the resulting spectrum is equal to the initial one).
2. To view the results of Bucket Integration applied to a series, from the Series menu, choose Table of Common Integrals. For the current example, do not enable this option. 3. Click OK to apply changes. Starting from version 10.0, ACD/1D NMR Manager allows you to specify the name and location of the .ESP file containing the temporary spectrum of sum or projection (with Intelligent Bucketing applied) whose integral ranges you want to apply to the current spectral document:
To select a file, either choose it from the File Name list or click Browse and specify its name and location in the Select File Name dialog box. Also, you can apply intelligent bucketing to thousands of spectra using the corresponding macros. For more information on how this can be done, refer to Section 8.7.
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4.6.5 Automatic Integration

The fastest and more convenient way to integrate spectral curves is automatic integration. 1. Before proceeding to the next step, on the Integration toolbar, click Delete All Integrals Curves . or select all of the integrals and click Delete Selected Integral
Tip To temporarily hide integral curves, on the General toolbar, release Show Integral
Curves
. . The program automatically integrates
2. On the Integration toolbar, click Auto Integrate regions containing signals.
3. You can remove the integrals for smaller values. Select the integral curve by clicking it, and then click Delete Selected Integral Curves .
4.6.6 Setting Reference Value

Now a reference point value can be specified: 1. Place the mouse pointer over the integral curve that will be the reference, e.g., the segment around 4.8 ppm, and then click to select it. 2. In the Reference Integral box on the Integration toolbar, type or select the assumed number of atoms . You can do this either by typing and pressing ENTER or by clicking the arrows to the right of the field. Note that all the other integrals are recalculated relative to the entered value. 3. Click Accept Changes to save the integral curves and quit this mode.
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4.6.7 Changing Integral Appearance

You can change the color of integral curves, as well as size, font, and orientation (vertical or horizontal) of integral values. 1. From the Options menu, choose Preferences, and then switch to the Integrals tab:
2. If necessary, change the color of integral curves, size, font and orientation of integral values, as well as the display accuracy of values, and click OK to apply the changes and close the dialog box.
4.7 Peak Fitting

This mode allows you to model a spectrum curve with a sum of analytic peak functions (Gauss, Lorentz or a mixture of both). Peak parameters can be adjusted during the optimization based on the Levenberg-Marquardt algorithm 1 to provide the best fit of the calculated spectrum to experimental data points. The Peak Fitting tool finds the most use for resolving overlapping peaks and defining more precise peak parameters: position, height, and area. Note In this section, we are going to use the spectrum CATEC_FT.ESP used in the previous sections. Depending on the options you have applied to it when doing the previous exercises, the peak position may slightly differ from what you will see in the pictures below. To enter the Peak Fitting mode, on the Analysis menu, point to Peak Fitting, and then choose Enter Mode or, on the Operation toolbar, click Peak Fitting Fitting toolbar appears. . Note that a new Peak
William H. Press, Saul A. Teukolsky, William T. Vetterling, Brian P. Flannery, Numerical Recipes in Fortran 77: The Art of Scientific Computing (Vol. 1 of Fortran Numerical Recipes), Second Edition., Cambridge University Press, 1996, pp 678-683.
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4.7.1 Specifying Peak Fitting Options

1. Click Peak Fitting Options tab appears first: to display the corresponding dialog box. The Fitting
2. In the Default Peak Parameters area, specify the parameters (peak width and function) that will be applied to each peak added to a model. For the current example, set the Width to 2 and Function to Gauss+Lorentz with the Lorentz Fraction set to 0.5. 3. In the Limits area, restrict any variations in peak widths and positions during optimization. The Fit point option allows you to deresolve data during optimization. You can select every 2nd, 3rd, 4th, or 5th point of the spectrum region to be fit. This option can be used to accelerate optimization (though at the expense of precision). Normally, it is recommended to fit every point unless the spectrum has excessive resolution. 4. In the Upon Optimization area, set up some actions to be done as soon as optimization has been completed: sound beep, show protocol, and/or update the Table of Peaks with adjusted parameters. Your PC should have a functioning sound card for the sound beep option to work. The beep volume is controlled by the system settings, which may be viewed in the Control Panel. If the Update Table of Peaks check box is not selected, the results are placed into the Peak Parameters dialog box and can only be updated from there. Otherwise, all of the results are automatically updated when you leave the Peak Fitting mode by clicking Accept Changes .
Note
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5. Switch to the View tab and choose the curve elements to be displayed, as well as the color for each of them. You can also set the dark region colorcolor for the region outside of the Peak Fitting area. Select the Animate Optimization check box to display the current peak fitting "picture" at each iteration. This creates the animation effect which will allow you to keep track of the optimization process (however, this slows down the whole process).
6. Specify the options as displayed above and click OK.
4.7.2 Defining Region

Now we are going to define the region to be modeled. It is not recommended to apply Peak Fitting to the whole spectrum at once since it may take a long time. To show the capabilities of Peak Fitting analysis, we are going to apply it to the region from about 3.7 to 3.9 ppm. 1. Zoom in to the region from 3.7 to 3.9 ppm.
Tip If you have integrals or a structure attached to the spectrum, they may interfere into
your work. To temporarily hide these elements, from the View menu, choose Integral Curves or point to Chemical Structure, and then choose Show. 2. Make sure that no buttons are pressed on the Peak Fitting toolbar and drag over the region so that the region to be modeled is included in the dark region:
Tip You can also click Set Region for Optimization
to define the region. Or you can drag the borders of the dark region to expand or narrow the region to be processed.
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4.7.3 Optimizing
1. As you can see, only the peaks that were labeled are modeled. For the current example, you may have already noticed that there seem to be a couple of unresolved peaks around 3.82 ppm. These unresolved peaks were not labeled and were not included into the fitting equation. To add them, click Add/Remove Peaks to label it and add it to the model: , and then click the peak near 3.82
2. Now point to another shoulder of the peak at 3.82 ppm and click when it is highlighted:
Tip To insert a peak label for any spectrum point or peak shoulder, hold down SHIFT and
click the appropriate point. 3. As soon as all of the peaks are included in the model, click Optimize . Since the Animate Optimization option is enabled, you can view how the curve changes at each iteration. If the corresponding option has been selected in the Peak Fitting Options dialog box, the Optimization Protocol appears:
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4. Click OK to close it and view the results:
5. Open the Table of Peaks (by clicking Show Table of Peaks ) and scroll to the optimized peaks. The calculated parameters are placed into the columns marked with an asterisk (*):
Note
To get additional data on what each column of this table means, refer to the 1D NMR Processor & Manager Reference Manual (NMRMOD_R.PDF) located in the ACD/Labs documentation folder (\\DOCS).
4.7.4 Modifying Peak Parameters

If you find the results of automated peak fitting for some peaks inappropriate, you can modify peak parameters manually in one of the following ways.
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4.7.4.1 Using the Mouse

When no buttons are active (or pressed) on the Peak Fitting toolbar, zoom in to the peak of interest and drag the peak nodes:
To change peak position and intensity, point to the upper node of the peak so that the four-way arrow appears and drag left or right, up or down.
To change the peak width, point to the side node at peak half-height so that the two-way arrow appears and drag left or right.
To modify peak shape for peaks with the Gauss+Lorentz mixed function, point to any of the nodes at the base of the peak, and then drag up or down. This will gradually change the LF from Gauss function (LF=0) to Lorentz function (LF=1).
4.7.4.2 Using the Dialog Box

Right-click on any peak node to display the Peak Parameters at dialog box where you can enter the required values for the selected peak:
Selecting the Lock check box near the parameter will make this parameter unchangeable for both manual and automated peak fitting. Click OK to save the changes.
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4.7.4.3 Batch Modification

You can change the parameters not only for each peak individually but also as a batch within the selected region. 1. Click Parameters to display the following dialog box containing a list of peaks from the selected region and their parameters:
Parameters in this dialog box are always displayed in Hz regardless of the current view options. 2. To change a specific parameter for all peaks, click in the respective column header (though not all of the columns can be changed this way), then enter the new value in the box. Click OK to apply the changes. 3. To change only one parameter for a specific peak, double-click the corresponding table cell, and then redefine the value:
Note
4. If you click Update Table of Peaks, the specified parameters will be updated to the Table of Peaks into the columns marked with an asterisk (*). 5. Click OK to apply the changes and close the dialog box. 6. On the General toolbar, click Show Whole Spectrum 7. Click Accept Changes .
to save the results and quit this mode.
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4.8 Attaching Chemical Structure

When the structure is attached to the spectrum in the Processor window, certain associations can be made. For example, you can assign peaks or spectrum regions to portions of the structure, or you can use the information from the structure for defining multiplets. to switch to the ChemSketch 1. On the Window Switching bar, click ChemSketch window and make sure that you are in the Structure mode (if not, on the General toolbar, click Structure ).
. If there are any structures in the 2. On the right Reference toolbar, click ACD/Dictionary workspace, the program asks you if you want to search for the drawn structure. Click No. 3. Make sure that the default search settings in the ACD/Dictionary dialog box are set as follows:
4. In the Quick Search field, enter catechinic acid:
You will see the structure of catechin appear. 5. Click OK to copy the structure to the ChemSketch window and click in the workspace to paste the structure:
OH HO O OH OH OH H H Note It is recommended to use stereo bonds to draw hydrogens of the CH2 group explicitly for making the results of the assignment and verification procedures more evident. For more information on how to draw stereo bonds, refer to the ACD/ChemSketch Reference Manual (CHEMSK_R.PDF) located in the ACD/Labs documentation folder (\\DOCS).
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6. On the Window Switching bar, point to Processor and, from the shortcut menu that appears, choose the Attach structure to the current spectrum:
7. Click OK. You are switched to the Processor window, and the structure is associated with the spectrum.
4.8.1 Displaying a Structure in the Processor Window

Once the structure has been inserted into the Processor window, there are four ways to display it: As a floating box which can be moved with the mouse pointer; In a separate frame in the left-hand corner; In a separate frame in the right-hand corner; or In a pop-up window.
1. If you prefer to change the display, on the View menu, point to Chemical Structure, and then choose the appropriate way of display. For this tutorial, it is recommended that you choose Floating Window.
2. To move the floating window, point to it and drag. To resize it, place the mouse pointer over any corner or border of the window so that the arrows appear instead of the pointer, and then drag it to resize the structure as you want. You can fix the way a structure is displayed for other sessions with ACD/1D NMR Manager in the Preferences dialog box, Structure tab (from the Options menu, choose Preferences).
Note
To hide the structure (not to remove it), on the General toolbar, release Show Chemical Structure .
To remove the structure from the current spectral document, on the Edit menu, point to Chemical Structure, and then choose Clear
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4.9 Defining Multiplets

To define multiplets, you can use the interactive Multiplets mode. On the Operation toolbar, click Define Multiplets and Couplings is replaced by the Multiplets one. to enter the Multiplets mode: the Operation toolbar
This section covers material that appears, in part, in the movie 1dnmr_6.exe which can be downloaded from our Web site. Also, by default it is placed in the MOVIES folder at the time of installing ACD/1D NMR Manager. Note that starting from version 10.0, the Information panel will automatically appear each time you enter the Multiplet mode (until you select the Dont ask me again check box) allowing you to view the instructional movie right from the program interface.
4.9.1 Specifying Multiplets Analysis Options

1. On the Multiplets toolbar, click Options . On the Common Parameters tab of the Multiplet Analysis Options dialog box that appears, specify options as displayed on the picture below:
2. Switch to the Automatic Algorithm tab.
3. For the current example, make sure that the Resolve Overlapped Multiplets check box is cleared and, set other options as displayed on the picture above.
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4.9.2 Automatic Multiplet Building

ACD/1D NMR Manager allows you to define multiplets in a spectrum and specify coupling constants within each multiplet automatically. All you have to do is to click a single button! Let us practice this feature on the same spectrum (CATEC_FT.ESP or CATECIN.ESP) we used in the previous sections. Note Depending on the spectral file you will use to perform the following exercises, data shown in various tables and pictures throughout this section of the tutorial may slightly differ from those you can see on your screen. 1. After the required options for the multiplet analysis are specified, on the Multiplets toolbar, . The multiplets building procedure is completed and each click Auto Build Multiplets defined multiplet is assigned a proper label ranging from M00 to M12. The following message appears:
2. All of the attendant information on each multiplet is automatically transferred to the Table of Multiplets. On the General toolbar, click Show the Table of Multiplets inserted data meets your expectations: to check if the
Note
Move the mouse pointer to the multiplet and the corresponding line is instantaneously highlighted (outlined with red) in the Table of Multiplets. Alternatively, you can click a row in the Table of Multiplets, and the corresponding multiplet is highlighted on the spectrum.
Although automatic multiplet building is a convenient and energy-saving procedure, you will not always be satisfied with the obtained results. However, you can always make proper corrections using other multiplet-related tools that are described in Section 4.9.3 below.
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4.9.3 J-Coupler
This section covers material that appears in the movie 1dnmr_6.exe which can be
downloaded from our Web site. Also, by default it is placed in the MOVIES folder at the time of installing ACD/1D NMR Manager. The Multiplet and Coupling Constant feature allows you to define selected regions in the spectrum as multiplets and specify coupling constants within each multiplet.
4.9.3.1 Basic Multiplet Recognition

On the Multiplets toolbar, click Show/Hide J-coupler to display the Multiplet
and ) in the Multiplet Analysis Analysis dialog box. Use the Browse buttons ( dialog box to navigate to the Multiplet labeled M01. Note Alternatively, you can right-click the spectrum to display the shortcut menu, and then choose J-Coupler. However, the shortcut menu appears only if the Context menu option is selected on the Mouse tab of the Common Preferences dialog box.
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Let us look more closely at the results of the J-Coupler analysis: The current multiplet is identified as a doublet of doublets (dd parameter is reflected on the button at step 3): with = 2.35 ppm: .
and two coupling constants are extracted: J1 = 16, J2 = 8.1 Hz:
The number of protons parameter (H) allows you to specify how many protons should be attributed to the current multiplet under examination. In the current example, this parameter is automatically defined as 1:
To ensure that the extracted chemical shift and set of Js are correct, the stick model and the baseline are calculated for the selected region. Note that the intensities of the red lines are calculated using the first-order approximation and are equal, even though the heights of the real peaks in the M1 multiplet are not the same (due to the so-called roof effect):
The J-Coupler counts the number of protons found in the spectra. In the Chemical Structure subwindow, you can view the overall number of protons (fourteen in this case) and information that is available from the attached structure. The box can be edited manually. The Protons Found parameter allows you to specify how many protons should be attributed to the multiplet under examination. In the present case, there is only one associated proton, but it is not defined as found since we have not updated the data to the program yet:
Note
If there is no attached structure, the number of protons in the molecule is set to 99.
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4.9.3.2 Defining Multiplets Using J-Coupler

Let us check if all of the multiplets have been properly defined. Zoom in the area around the first multiplet labeled M01. Use the Browse buttons on the Multiplet Analysis dialog box ( ) to navigate through the multiplets: and
As we move on, we find out that the multiplet labeled M09 has been improperly defined. Actually, these are two doublets rather than one multiplet. In this case, we will have to resort to other tools from the Multiplet kit to correct it manually.
1. In the Multiplet Analysis dialog box, click Delete Multiplets DELETE.
to delete this multiplet.
Tip Alternatively, to delete a multiplet, on the General toolbar, click Show Table of
, click the corresponding row in the Table of Multiplets, and then press
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2. Move the mouse pointer to the starting point of the multiplet and select it by dragging:
3. As you release the mouse button, information on the defined multiplet is automatically appears in the Multiplet Analysis dialog box:
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The current multiplet is identified as a doublet (d parameter is reflected on the button at step 3) and a coupling constant J1 = 1.9 is extracted. Tip The coupling constant value can vary depending on the current value of the Points Count parameter that you can see in the Parameters panel (from the View menu, choose Spectrum Parameters). Note that ACD/1D NMR Manager automatically analyzes multiplets when specifying multiplets ranges and updates the Table of Multiplets with corresponding data.
4.9.3.3 Setting Couplings Manually

The J-Coupler can perform much of the assignment work but in some cases where peaks are not labeled, differ considerably in height, or strongly overlap, you will have to intervene. 1. Select two peaks next to the multiplet M09 by dragging over them:
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The multiplet is labeled as M14 but remains undefined. The reason is inconsistent peak intensities, i.e., the heights of two peaks in this multiplet differ considerably.
2. In this case, you can define the coupling constant manually. Point to the peak labeled 6.70 until the vertical line appears on it, and then drag to the second peak within this multiplet:
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The coupling constant is now defined and automatically inserted into the J-Coupler dialog box:
The rest of the peaks are defined properly.
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4.9.3.4 Adding Missing Peaks

Although in our case, all peaks have been labeled on the spectrum, there might be spectra where some peaks are missing. This section shows you how to handle such a situation. and ) in the Multiplet Analysis dialog box, navigate to 1. Using the Browse buttons ( the M03 multiplet. The results of multiplet building are correct. However, let's imagine that two peaks within this multiplet have not been labeled:
no label
2. To remove a peak label, move the mouse pointer to the peak and double-click when it is highlighted. Note that the first click will exclude the current peak from the list of the multiplets peaks and the second click will delete the peak label. Using this procedure, remove the labels from both the peaks indicated by arrows in the picture above.
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Note that the multiplet is automatically recalculated and now J-Coupler fails to define the coupling pattern type:
3. Click the unlabeled peaks, one by one, to label them. Note that clicking an unlabeled peak will create a peak label and add it to the list of peaks of the current multiplet.
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4. The multiplet is defined as a triplet of triplets and the corresponding stick model is displayed.
5. Let us also recalculate the extracted J-values in accordance with the optimized spectrum curve.
6. In the Multiplet Analysis dialog box, click Delete
. In the Multiplet Analysis Options 7. On the Multiplets toolbar, click Options dialog box, select the Use Peak Fitting check box. Since the Peak Fitting was applied to the spectrum, this option becomes available. Click OK. 8. Drag over the peaks to define the multiplet once again and recalculate values of coupling constants; the stick model as well as the J1 and J2 values are recalculated in accordance with the optimized spectrum curve. Note that the Table of Multiplets is automatically updated. 9. On the General toolbar, click Show Whole Spectrum .
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4.9.4 Connecting Multiplets Manually

ACD/1D NMR Manager allows you to establish a local coupling network by connecting multiplets with each other where it is possible. to display the Multiplet Analysis 1. On the Multiplets toolbar, click Options Options dialog box, and on the Common Parameters tab, set the Coupling parameter to 0.5. Click OK to close the dialog box. 2. On the Multiplets toolbar, click Manual Connect Multiplets 3. Point to the multiplet M03 and click when it is highlighted: .
4. Drag the mouse pointer to the multiplet M01 and click when it is highlighted. As the selected multiplets have several unassigned constants, the Multiplets Coupling dialog box is displayed allowing you to resolve the ambiguity manually:
5. Select the coupling constants that are to be used for connecting the selected multiplets as displayed in the picture above, and click OK. 6. Connect multiplets M03 and M02 using the same procedure (steps 3-5).
Tip Only one coupling constant of the M03 multiplet should be assigned:
7. On the Multiplets toolbar, click Manual Connect Multiplets switch off this mode.
once again to
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4.9.5 Connecting Multiplets Automatically

1. On the Multiplets toolbar, click Auto Connect Multiplets . As a result the Information message appears informing you that 8 multiplets connections have been defined:
2. On the General toolbar, click Show Table of Multiplets connections are formatted with bold:
. Note that the manually made
3. Right-click in the Table of Multiplets and, from the shortcut menu that appears, choose Expand Table to display information on each coupling constant in a separate row.
Tip It is highly recommended to use the expanded table view for deleting and/or
approving the ambiguous connections. 4. Right-click on the row corresponding to M07 and, from the shortcut menu, choose Approve Connection. The ambiguous connection between M06 and M07 is approved:
Only the manually inserted, approved and reliable connections are taken into account during the auto assignment and verification procedures if the Check Coupling Network check box is selected in the Assignment Options dialog box. 5. On the View menu, point to Tables, and then choose Multiplets to close the Table of Multiplets. 6. On the Multiplets toolbar, click Accept Changes mode. to save changes and quit the Multiplets
Note
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4.10 Assigning Peaks and Verifying the Structure
This section covers material that appears in the movies 1dnmr_2.exe and 1dnmr_5.exe
which can be downloaded from our Web site. Also, by default they are placed in the MOVIES folder at the time of installing ACD/1D NMR Manager. After you insert the structure, you can assign its atoms to peaks or regions or you may "verify" the structure to determine the degree of correspondence between the structure and the corresponding spectrum (the verification is only available for HNMR spectra). Not surprisingly, the automatic assignment of peaks and structure verification can be a difficult undertaking for any software. 1D NMR Manager does not, by default, include these options in its basic form. The Auto Assign and Verification features are driven by the same prediction engine that is used in our NMR Predictor software. The Auto Assign and Verification capabilities are additional options that should be purchased along with 1D NMR Manager (or SpecManager). ACD/C+H NMR Predictors and DB permits user training of the parameter file on which the calculations are based to improve prediction accuracy. In 1D NMR Manager, using the Spectra Calculation dialog box (Options menu), you can specify your own database files to be used for calculations during assignment. For more information on how to create these databases and how to work with them, refer to the NMR Databases Users Guides and HNMR Predictor Users Guide. Note We present Auto Assign and Verification options in this portion of the tutorial to show you just how powerful and time-saving these features can be. On the Operation toolbar, click Assign Peaks, Regions, and Multiplets to Structure . Note that a new Assignment toolbar appears and the By Multiplet tool ).
is activated automatically (
4.10.1 Verification
We will start with the verification procedure to evaluate the correspondence between our chemical structure and experimental spectrum: to display the 1. On the Assignment toolbar, click Auto Assignment Options Assignment Options dialog box where you can set options for verification and automatic assignment.
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2. In the Create Automatic Assignments area, select the Show Calculated Spectrum check box and make sure that the All option is selected.
3. Click Advanced Assignment Options and, in the dialog box that appears, change the values as shown in the picture below. Note that Shift Tolerance and Shift Looseness denote the minimal and maximal acceptable error for calculated chemical shifts. In the Quantitative Parameter box, select Number of Nuclei to define the source of Quantitative Weight factor.
For more information on the Advanced Assignment Options dialog box, refer to the ACD/1D NMR Processor & Manager Reference Manual (NMRMOD_R.PDF) located in the ACD/Labs documentation folder (\\DOCS).
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You should also set proper options for the spectrum that will be calculated after verification. 4. From the Options menu, choose Spectra Calculations to display the Calculation Options dialog box. On the Calculation tab, set the options as shown in the picture below. Make sure that the Calculate J-values check box is selected. Select both the HP and HF check boxes to use heteroconstants in calculations.
5. Make sure that the Use Solvent from Spectrum Parameters check box is selected and actual solvent specified in the Parameters panel will be used. 6. Switch to the Shape tab, and then set the following options:
Note that the Common Width parameter is set equal to 2spectrum line width corresponding to the average of the FWHH parameter as specified after Peak Fitting in the Table of Peaks.
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To visualize the quality of the match for each atom on the attached structure: 1. From the Options menu, choose Preferences, and in the 1D NMR Preferences dialog box, switch to the Structure tab. 2. Make sure that the Show on Structure check box is selected in the Assignment Quality View area. Choose the Verification Match Factor option and click the adjacent Browse ). button ( 3. In the Assignment Quality View dialog box that appears, specify the following boundary values:
4. To start verification and automatically assign peaks to a structure, on the Assignment toolbar, click Verification . As a result of the verification procedure, a spectrum is calculated and displayed together with the experimental one in the Tile view mode. The Verification Result panel appears, showing the Match Factor, RMS of Assignment, Structure Purity, and Reliability, and also evaluating the result of the verification as Good, Middle or Poor.
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5. Click OK to close the panel. Note that the information on the status and result of verification together with HNMR Match Factor, HNMR Reliability, HNMR RMS of Assignment, and HNMR Structure Purity values are added to the User Data panel (from the View menu, choose Spectrum User Data). Note that if the structure attached to the spectrum is considered inconsistent, clicking OK in the Verification Result dialog box will display the Verification Diagnostics panel which contains detailed message(s) on the problem(s) that occurred during the verification procedure. For more information on all possible messages, refer to the ACD/1D NMR Processor & Manager Reference Manual (NMRMOD_R.PDF) located in the ACD/Labs documentation folder (\\DOCS). Tip If the Reliability value is less than 35%, the results of verification cannot be estimated as good, middle or poor and the question mark will be displayed on the Verification Result panel. This means, that there is not enough spectral data used for calculating Match Factor (for example, due to the overlapped peaks). During the verification procedure, ACD/1D NMR Manager automatically performs integration of the predicted spectrum and defines coupling patterns of the protons that strongly interact, so the integral curves and multiplets are displayed on the calculated spectrum.
4.10.1.1 Dealing with Verification Results

Now, you can check how the peaks are assigned to the structure by moving the mouse pointer either over the structure or peaks:
You can change the color of the assigned atoms and assignment correlations on the Structure tab of the Preferences dialog box. To display this dialog box, from the Options menu, choose Preferences. Although both spectra are quite similar, they have different heights because the experimental spectrum contains the peak annotated as HDO that is much higher than the rest of the peaks. Naturally, there is no corresponding peak in the calculated spectrum.
Note
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Note that the experimental and calculated spectra are synchronized during the verification on the General toolbar). That means that when process (the Synchronize button is active you change the height of the shaded area in the zoom window at the top, the peak height of both spectra changes accordingly. Move the mouse pointer to the frame bounding the shaded area until the two-way arrow appears, and then drag either up or down. Note that both spectra are zoomed in or out accordingly:
Drag up or down to vertically zoom out or in respectively. To navigate to another group of peaks, point to the inside of the shaded area, and then drag left or right.
It is also possible to view the corresponding peaks in the experimental spectrum and in its calculated counterpart. Move the mouse pointer to a peak in one of these spectra to view the corresponding peak in the other:
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4.10.2 Manual Assignment

During the verification procedure, peaks are automatically assigned to the corresponding atoms. However, if you do not want to perform verification and instead, manually assign the peaks, use the following procedure: 1. On the Assignment toolbar, click Clear Assignment Table assignments made in the current spectrum. to remove all of the and
2. Zoom in the region for a better view. On the General toolbar, click Manual Zoom enter the following coordinates for the region to be enlarged:
3. Click OK to enlarge the region. 4. On the General toolbar, click Show Atom Numbers structure if they are not already displayed. to display the atom numbers on the
4.10.2.1 Assigning by Peak

Now we are going to assign the peaks to atoms. To practice this option, try to assign the peaks from the leftmost portion of the spectrum to atoms 18, 19, and 20. Note that the numbering of the structure attached to the spectrum and the offset value of the peaks may be different than described here. 1. On the Assignment toolbar, click Assign By Peak .
2. Click the peak at about 8.82ppm that is to be assigned. Move the mouse pointer to the atom 18 until it is highlighted and click:
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3. Now click the atom 19, drag to the peak at about 8.87 ppm and click when it is highlighted with red:
4. In the same manner, assign atom 20 to the peak at about 8.94. As a result, you should obtain something like the following:
5. On the General toolbar, click Show Whole Spectrum
4.10.2.2 Assigning by Multiplets

If you have defined any multiplets as described in Section 4.9, you can also assign them to the structure atoms manually. Note that starting from version 9.0, the coupling-guided manual assignment is available. 1. On the Assignment toolbar, click Assign by Multiplet .
2. Point to the multiplet M03, and click when it is highlighted. Note that the Multiplet Assignment Preview allows you to estimate the quality of potential assignment at once by coloring all the protons on the chemical structure.
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3. Move the pointer to the atoms 4a and 11. Note that the number of expected and found coupling constants (J) is different:
4. Now move the mouse pointer to atom 5. The number of Js Found corresponds to Js Expected and the atom is highlighted with green, so click on it to assign:
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5. Using the same procedure, assign multiplet M02 to the 4b atom:
The green arrow between atoms 4a and 5 indicates that the constant value between these atoms agrees with the distance between them.
4.10.3 Automatic Assignment

During the verification procedure, peaks are automatically assigned to the corresponding atoms. However, if you do not want to perform verification and wish rather to perform automatic assignment as such, use the following procedure: 1. On the Assignment toolbar, click Auto Assignment Options Assignment Options dialog box. to display the
2. Select the Keep Assignment check box, to keep the manually made assignments during the automatic assignment procedure. 3. Cancel the selection of the Show Calculated Spectrum check box, and then click OK. . The program starts calculating spectra for the given structure 4. Click Auto Assignment and correlates experimental and calculated spectra. 5. Move the mouse pointer over the structure or the spectrum plot to view the assigned peaks.
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6. On the General toolbar, click Show Table of Assignments to display the Table of Assignments. Note that information on the assignments that were made manually by using the Assign by Multiplets tool is formatted bold:
7. On the Assignment toolbar, click Clear Assignment Table assignments made in the current spectrum.
to remove all of the
4.10.4 Comparing Manual and Automatic Assignments

If you are not sure that the manually made assignment is quite correct, you can compare it with the automatic one in the side-by-side window. 1. First let us create a deliberately false assignment. For this purpose, on the Assignment toolbar, click Assign by Multiplet . 2. Assign a multiplet to an atom (for example, M03 to 4b) using the procedure described in Section 4.10.2.2. 3. On the Assignment toolbar, click Auto Assignment Options Assignment Options dialog box. 4. Select the Enhanced Verification check box, and click OK. to display the
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5. On the assignment toolbar, click Verification . As a result of the verification procedure, the Enhanced Verification dialog box is displayed allowing you to visually compare the results of verification based on the manually and automatic assisted assignment:
6. Click the structure with the automatically assisted assignment which is more accurate to select it. Note that the selected structure is framed in red and the OK button became available. 7. Click OK to accept the currently selected result of verification and close the dialog box.
4.11 Shortcut Mode

The Shortcut mode was designed to create a very easy workflow that allows you to manually process a 1D NMR spectrum as quickly as possible.
This section covers material that appears in the movie 1dnmr_9.exe which can be
downloaded from our Web site. Also, by default, it is placed in the MOVIES folder at the time of installing ACD/1D NMR Manager. The Information panel will automatically appear each time you enter the Shortcut mode (until you select the Dont ask me again check box) allowing you to view the instructional movie right from the program interface. To demonstrate some Shortcut mode capabilities, we will use the HNMR spectrum of catechin.
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Please take a moment to open FID file located in the EXAMPLES\SPECMAN\1DNMR\CATECHIN.FID folder:
4.11.1 Specifying Shortcut Mode Options

Prior to start working in the Shortcut mode, let us specify some processing steps that are to be automatically applied to the spectral document on entering and quitting this mode. 1. From the Options menu, choose Shortcut to display the Shortcut Mode dialog box. 2. In the Actions upon entering Shortcut mode area, select all the check boxes except for Zero Filling and Detect strong extraneous signals. 3. In the Actions upon exiting Shortcut mode area, select the Save As check box for the program prompts you to save the processed spectral document to a new file on disk on quitting the Shortcut mode. As a result the Shortcut Mode dialog box should look like the following:
Tip To automatically create either a standard or template-based report in
ACD/ChemSketch that will include your fully processed spectrum, chemical structure, multiplet report, and any other data on quitting the Shortcut mode, select the Report check box.
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4. After all the desired settings are specified, click OK to close the dialog box. 5. On the Operation toolbar, click Shortcut Mode explains what this mode can be used for, click OK. . In the Information panel that
If you have specified the Shortcut Mode options as displayed above, the FID with the previously applied weighting function is instantaneously Fourier Transformed, phased, and baseline corrected:
Now using the standard mouse actions, you can label peaks, define multiplets, insert annotations, etc.
4.11.2 Action Helper

First, using the Action Selector panel that appears on entering the Shortcut mode, let us specify the processing operations that are to be performed on the specific mouse actions. Tip The Action Selector panel is automatically displayed on entering the Shortcut mode if the Show Action Selector check box has been selected in the Shortcut Mode dialog box (step 3 of the previous section). Click the arrows and, in the boxes to the right of the corresponding actions, and specify the Software Response parameters as displayed in the picture below:
For more information on this panel, refer to ACD/1D NMR Manager and Processor Reference Manual (NMRMOD_R.PDF) located in the ACD/Labs documentation folder (\\DOCS).
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4.11.3 Defining Dark Region

In this spectrum there is a rather large water peak that is not relevant to the characterization of this compound. We should remove this peak from consideration first. 1. On the General toolbar, click Horizontal Zoom area to enlarge it: , and drag over the corresponding spectral
2. Drag over the peak. As you release the mouse button, the software will ask you of whether you want to create a multiplet or annotate the peak. Select Annotate / Set Dark Region.
3. In the Edit Annotation dialog box that appears, type Water (the name of the impurity), select Add as Dark Region check box, and then click OK. 4. In the Edit Dark Regions dialog box that appears, verify the dark region settings and click OK.
Note that this region will be excluded from any other processing steps to be performed with this spectrum. To edit the specified dark region, just click it and, from the shortcut menu that appears, choose the required command. Note Dark regions can be detected automatically on entering the Shortcut mode if strong extraneous signals are present in the spectrum (TMs, DMSO, water in dmso or methanol) and the corresponding check box selected in the Shortcut Mode dialog box. 5. On the General toolbar, click Show Whole Spectrum .
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4.11.4 Setting Reference Point

Now let us reference the spectrum. 1. On the General toolbar, click Rectangular Zoom region from 2.0 to 3.0 ppm: , and drag to enlarge the spectrum
2. Move the mouse pointer to the peak to be set as a reference point (in our example, it is the small peak around 2.48) and click when it is highlighted.
3. In the Solvent Shifts dialog box that appears, choose DMSO-d62.50 from the list and select the Add Annotation check box. For more information on this dialog box, refer to ACD/1D NMR Manager and Processor Reference Manual (NMRMOD_R.PDF) located in the ACD/Labs documentation folder (\\DOCS). 4. Click OK to close the dialog box and reference the spectrum:
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4.11.5 Defining Multiplets

Now we can manually define the multiplets in this spectrum. 1. In the Action Helper panel, specify the Define Multiplet and Integral parameter as a software response to the Select Area action:
2. Move the mouse pointer to the starting point of the multiplet and select it by dragging. For the current example, drag over the region 2.29..2.38 ppm to define the first multiplet:
3. As you release the mouse button, the annotation showing the defined multiplet automatically appears:
The current multiplet is identified as a doublet of doublets (dd parameter is displayed in the multiplet label) and coupling constants J1 = 16 and J2 = 8.1 are extracted. Note You can adjust the reference value of the integral curve that appears immediately as you define a multiplet. Click its label and specify the assumed number of atoms in the Integration Reference dialog box that appears. All other integrals will be recalculated relative to the entered value.
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4. Since there is no structure attached to the spectral document, the number of protons is incorrectly identified. Click on the defined multiplet and, in the H box of the Multiplet Analysis dialog box that appears, type 1:
You can edit a multiplet in the Shortcut mode via the Multiplet Analysis dialog box which appears when you click the multiplet if Edit Multiplet is selected as a Click on Multiplet parameter in the Action Selector panel. 5. Use the same procedure, to define the second multiplet in range from 2.60 to 2.7 ppm:
Note
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6. On the General toolbar, click Show Table of Multiplets
to display the following table:
7. Right-click within the Table of Multiplets and, from the shortcut menu that appears, choose Close Table.
4.11.6 Assigning Multiplets

The Shortcut mode allows you to assign any spectral segment defined as a multiplet to an atom of the structure. To perform this operation, we should attach a chemical structure first. 1. Take a moment to attach the structure of catechin to the current spectral document. For more information on how this can be done, refer to Section 4.8. 2. On the General toolbar, click Show Atom Numbers .
3. In the Action Helper panel, specify the Start Assignment parameter as a software response to the Click on Multiplet action: 4. Point to the multiplet M01, and click when it is highlighted with red. 5. Move the pointer to the atom 4a and click on it to assign:
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6. Using the same procedure, assign multiplet M02 to the 4b atom::
Note that after assignment is performed the corresponding atoms are highlighted with green (the Assigned Atoms color is specified on the Structure tab of the 1D NMR Preferences dialog box, Options menu). to display the Table of 7. On the General toolbar, click Show Table of Assignments Assignments. Note that information on the assignments that were made manually is formatted with bold:
8. Close the Table of Assignments.

Important Using other parameters of the Action Selector panel, you can also insert and
delete peak labels, annotate spectral peaks and regions, and edit defined multiplets in the Shortcut mode.
4.11.7 Quitting Shortcut Mode

1. On the Operation toolbar, click Shortcut Mode mode. once again to quit the Shortcut
2. According to the options specified in the Shortcut Mode dialog box (see Section 4.11.1), the Save As dialog box automatically appears. 3. Specify the name and location of the .ESP file to which the processed spectral document is to be saved, e.g., CATEC_FT1.ESP, and click Save. 4. To complete the current example, from the File menu, choose Close.
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5. Multispectral Operations
5.1 Objectives
ACD/SpecManager allows you to perform various multispectral operations with two or more spectra at a time. The processing modules of SpecManager provide great flexibility when working with data because you can load and compare many spectra at once, even with different spectroscopic techniques, if you have the requisite modules. For example, the 1H NMR, 13 C NMR, and mass spectrum of the same compound can be displayed simultaneously if you have installed 1D NMR Processor and MS Processor in the same folder. In this chapter, we ask you to practice the following multispectral operations on two NMR datasets that you have loaded: Displaying spectra in the Tile vs. Full mode; Adding, deleting, and replacing spectra; Summarizing displayed spectra through the Table of Windows; Synchronizing two spectra; and Performing arithmetic on two spectra. Arithmetic operations can only be applied to spectra of the same nucleus type and having the same frequency. Spectra can have a different number of points and width or can be shifted relative to each other along the Y-axis. In this chapter, as an example, we are going to use the spectrum of D2O with acetonitrile (MULTI_1.ESP) and the spectrum of sucrose solution in that solvent (MULTI_2.ESP) from which the spectrum of pure solvent was subtracted, so that signals of D2O and acetonitrile are negative. Both spectra have different widths and are shifted relative each other, so first we will apply the synchronization and then add one spectrum to another.
5.2 Loading Two Spectra

1. If there are any spectra open in the Processor window, from the File menu, choose Close All. 2. In the upper right-hand set of multi-spectrum buttons, make sure that the New Window and Tile modes are on. 3. From the Windows menu, choose Set Scrolling and make sure the number of windows to be displayed at a time is set to higher than two. and find the MULTI_1.ESP and MULTI_2.ESP files in the 4. Click Open/Import Spectrum example folder. Open them one at a time.
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5.3 Synchronizing Spectra

Sometimes spectra that you want to compare belong to different ranges of X. Clicking Synchronize will allow you to represent spectra in a form convenient for comparing them:
1. In the upper right-hand set of multi-spectrum buttons, make sure that the New Window and Tile modes are on. 2. From the Windows menu, choose Set Scrolling and make sure that the number of windows to be displayed at a time is set to higher than two. 3. If MULTI_1.ESP and MULTI_2.ESP are not currently open, click Open/Import Spectrum , find and open the files located in the example folder. 4. Click the window tab containing the spectrum from the MULTI_2.ESP file to make it active, then while holding down SHIFT, click the tab of another window to select it (the active window tab is marked with a red cross). 5. On the right-hand side of the General toolbar, click Synchronize are now synchronized.
Note
. Note that both spectra
If you apply Horizontal Zoom with this button active, all of the selected spectra will be zoomed simultaneously. 6. From the View menu, choose Cursor to display a vertical line which makes a comparison more obvious.
Note
The cursor can also be synchronized with 2D NMR spectra. For more detailed information, refer to the ACD/2D NMR Reference Manual and Tutorial located in the ACD/Labs documentation folder (\\DOCS).
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5.4 Arithmetic: Adding and Subtracting Spectra

As soon as the spectra are synchronized, we may proceed to perform various arithmetic operations (adding and subtracting) with several spectra at a time. Arithmetic operations can only be applied to spectra of the same nucleus type and having the same frequency. Spectra can have a different number of points and width or can be shifted relative each other along the Y-axis. 1. Make sure that both spectra are selected as described in the previous section. One of them (MULTI_2.ESP) should be active, as shown by a dark-blue tab:
2. From the Process menu, choose Arithmetic. A new toolbar appears:
3. Click Add Spectrum MULTI_2.ESP.
and the MULTI_1.ESP spectrum will be added to the
The sum is calculated by the following formula: Sum = A + k*B, where A is the spectrum (MULTI_2.ESP) to which we are adding spectrum B (multi_1.esp) and k is a multiplier that can be specified in the field on the toolbar. 4. Set the coefficient k to 0.06 in the ENTER. field by typing in the text box and press
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5. Press PAGE UP several times to zoom in the spectrum. As you can see, the peaks of D2O and acetonitrile have completely disappeared:
Note
If you click Add Spectrum to deselect it, the results of adding will be canceled. If you want to set the results, for example, in order to do subsequent additions or subtractions, click Fix Result . and zoom out the spectrum.
6. To save the resultant spectrum, click Accept Changes

Note
In a similar manner, you may apply Subtraction by clicking Subtract Spectrum .
5.5 Working with Spectral Series

5.5.1 What is a Series?
A series is two or more spectra that are placed in one spectral window. In ACD/1D NMR Manager, only spectra of one type (either 13C or 1H) can be placed into one spectral window. Spectra that are included in a series may have different units along the X-axis, but, if grouped in a series, they will all be displayed in one of the supported units of measurement (ppm, Hz, or pts). Each spectrum that is placed into a series retains its properties: spectrum parameters, spectrum user data and structure user data (if any), custom color, peak labels, assignments, and annotations. You can apply any processing and analysis operations to any individual spectrum in a series. Some of the processing operations can be applied to an entire series of spectra at a time as soon as you enter the Group Treatment mode ( ).
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5.5.2 Creating a Series

For the current example, we are going to use the files located in the ACD/Labs examples folder, EXAMPLES\SPECMAN\1DNMR\SERIES. 1. Close all of the spectra without saving any changes. and Tile to activate the corresponding 2. On the General toolbar, click Add Mode modes. The Add mode signifies that each subsequently loaded spectrum will be added to the same window. 3. On the General toolbar, click Open/Import Spectrum to display the Import dialog box.
4. In this dialog box, find the location of the following files 1.ESP, 2.ESP, 3.ESP, 4.ESP, and 5.ESP. 5. Select them by clicking their names while holding down SHIFT, and then click Open. When you release the mouse button, the spectra are placed into one window as a series. 6. To specify the spectra offset relative each other, from the Series menu, choose Offset. In the dialog box that appears, set X Offset to 0.15 and Y Offset to 0.2, and then click OK:
Tip Alternatively, you can arrange spectra of a series in the workspace manually. On the
series menu, point to Manual Offset, choose Enter Mode, and then just drag a spectrum to the desired location. By default, the active spectrum is displayed in the Active color specified on the Spectrum tab of the 1D NMR Preferences dialog box and the rest of the spectra are shown in contrasting auto colors. To change the color of the active spectrum, from the Options menu, choose Preferences, and then on the Spectrum tab, change the color. Note Other ways of adding spectra to a series are described in the next section.
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7. From the Series menu, choose Table of Spectra to display the table containing information on the spectra in a series:
The information on the currently active spectrum is formatted with bold and the Visible box is not available. To manage the contents of the table, use the commands from the shortcut menu (this menu can be displayed by right-clicking on the table). 8. Save the series of spectra in a separate file. From the File menu, choose Save As and specify a new name for it, for example, SERIES1.ESP, then switch back to the New Window mode .
Note
5.5.3 Creating a Series in Other Ways

This section outlines the other ways to create a series of spectra. If you are comfortable with the method described above, skip this section. Adding the spectra one by one: 1. In the empty Processor window, click Add Mode to switch to the corresponding mode.
to display the Import dialog box. 2. On the General toolbar, click Open/Import Spectrum In this dialog box, specify the location of a file containing a spectrum that should be included in the series, and then click Open. 3. Repeat step 2 until all of the spectra are added to the series. Adding spectra from a database: 1. In the Processor window, activate the Add mode. 2. Switch to the Database window and open the required database. 3. Browse through the database to find the required record. Double-click the Plot subwindow to transfer the spectrum from the database to the Processor window. 4. Switch back to the database and repeat the above step until all of the desired spectra are added to the series.
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Collecting spectra into a series: Suppose you have several processed spectra open in separate windows either in the Tile or Full view mode and you want to form a series of them: 1. Select the required windows by holding down SHIFT and clicking their tabs.
Tip In the Full view mode, the names of the selected windows are light-blue, the name of
the active window is emphasized in bold:
Tip If you want to cancel the selection, from the Windows menu, choose Unselect All.
2. From the Series menu, choose Collect Spectra, the program will add the spectra from the selected windows into a new one to form a series. A new window has a default name, e.g., noname00(1).
5.5.4 Coloring Spectra

One of the spectra within a series is considered active, and is distinguished by an "active" color (in the above example, it is black). The structure and the tables displayed in the Processor window relate specifically to that active spectrum. Depending on the option selected in the 1D NMR Preferences dialog box (Options menu), other spectra in a series (that are not active at the moment) may be represented in system color (all spectra are displayed in one color), auto colors (different colors are automatically assigned to the spectra), or in their custom colors (user-defined colors assigned to the required spectrum(a)). Note that the custom color specified for a spectrum is an inherent property and is stored with the spectrum when it is saved, placed to the databases or reported to the ChemSketch window. Note When saving spectral documents and creating reports, the specified custom colors will be used regardless of the coloration scheme currently applied. The active spectrum always preserves the active color (from the Options menu, choose Preferences to change the Active color). To view the color of the active spectrum, switch to another spectrum in the series.
5.5.4.1 Applying Auto Colors

At first we will automatically assign different colors to the spectra in the current series. 1. From the Options menu, choose Preferences. In the 1D NMR Preferences dialog box, on the Spectrum tab, make sure that the Apply System Colors check box is not selected. 2. On the Series menu, point to Coloration, and then choose Auto Colors. In case you are not satisfied with the auto colors applied by default, you can edit them at will. 3. From the Options menu, choose Autocoloring to display the corresponding dialog box:
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4. From the color palette, select the color for the first spectrum in a series, and click Set . The color of the first row of the table changes.
5. Select the second row and repeat the previous step. Change the colors for the required number of spectra. For the current example, specify the desired colors for five spectra, you may wish to use the following contrasting colors:
6. Click Apply and then click OK:
Later, to apply the selected colors to the spectra in a series, on the Series menu, point to Coloration, and then choose Auto Colors. The colors specified in the Autocoloring dialog box will be used.
5.5.4.2 Applying System Color

Now we will color all the spectra of the series in one system color. 1. On the Series menu, point to Coloration, and then choose System Colors. 2. From the Options menu, choose Preferences. On the Spectrum tab of the 1D NMR Preferences dialog box, in the System color box, select the desired color. 3. Click Apply and OK to apply the specified color to the whole series.
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5.5.4.3 Applying Custom Colors

To define custom colors that will be used when saving the series or creating reports, follow the procedure: 1. From the Options menu, choose Preferences. On the Spectrum tab, in the Coloration area, select the Apply Custom Colors check box. 2. From the Series menu, choose Table of Spectra. 3. In the Table of spectra, double-click the color box of the required spectrum. Choose the desired color from the color palette. 4. Repeat the previous step until all of the spectra in a series have the desired colors. Later, to apply the selected colors to the spectra in a series, on the Series menu, point to Coloration, and then choose Custom Colors. The colors you have specified will be used.
5.5.5 Copying, Moving, and Deleting Spectra from a Series

The program allows you to operate spectra in a series in the following ways: 1. Double-click 5.ESP in the Table of Spectra to make it active. 2. From the Series menu, choose Copy Spectrum. The active spectrum is copied to a separate window and preserved in the series:
Note that a spectrum copied from a series into a new window is considered as created and has a default name, e.g., noname01(2). Tip If you want to remove a spectrum from a series and place it in a separate window, from the Series menu, choose Move Spectrum. To delete a spectrum completely, from the Series menu, choose Delete Spectrum. 3. When several windows are displayed as tiled, the horizontal scale beneath each window may be superfluous. To hide the horizontal scale in the upper window, make that window active (click its tab) and, from the Options menu, choose Preferences. 4. In the Preferences dialog box that appears, on the Spectrum tab, clear the Horizontal Scale check box and click OK. The horizontal scale will be hidden.
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5.5.6 Processing Spectral Series

The Group Treatment tool makes it possible to apply some of the processing options to all spectra in a series at once. to make the Full mode active. If there are any spectra 1. On the General toolbar, click Full open in the Processor window, close them; from the File menu, choose Close All. 2. Click Open/Import Spectrum and find an FID file in the SERIES folder.
3. Make sure that the Group Treatment mode series are active. 4. On the Operation toolbar, click Zero Filling box, set the Points Count to 4096.
is on. Note that all of the spectra in the , and then in the Zero Filling dialog
5. Click OK, and you will see that all of the spectra are modified. 6. Before proceeding to Fourier transform, it is recommended that you multiply the spectra by a window function. Click Window Functions dialog box. to display the Window Functions
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7. For the given example, select Exponential, and in the line-broadening (LB) box, specify a value of 1.
8. Click OK to start processing. Note that the FIDs is somewhat modified. 9. On the Process menu, point to Fourier Transform, and then choose Default Transform. The display will change markedly:
10.From the Series menu, choose Offset, and then specify the values as follows:
11.On the Series menu, point to Coloration, and then choose Auto Colors to apply the colors specified in the Autocoloring dialog box (Section 5.5.4) to the spectra. 12.On the Operation toolbar, click Peak Picking toolbar. 13.On the Peak Picking toolbar, click Adjust Peak to display the Peak Picking .
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14.Move the mouse pointer to a peak at about 1.39 ppm and click when it is highlighted. Note that all of the spectra in the series are labeled.
Tip If you cannot see the labels, on the Series menu, point to Show Labels, and then
choose Peaks.
15.Click Accept Changes
to save the changes made and quit this mode.
You can also apply other processing operations: phase correction, baseline correction, reference setting, and peak integration to the entire series of spectra. To get more information on the operation of those options, refer to Chapter 3.
Note
You can apply the processing operations to a single spectrum of a series. Disable the Group Treatment mode by clicking Group Treatment desired spectrum active with the help of the arrows , and then make the .
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6. Quanalyst
6.1.1 Objectives
This chapter will familiarize you with ACD/Quanalyst. The Quanalyst instrument is intended for retrieving a variety of spectral properties relating to peaks, multiplets, integrals, spectrum parameters, and spectrum user data, and performing arithmetical calculations with the obtained results via the Quanalyst dialog box. The focus of quantitation is to calculate spectral response and display various correlations. The most widespread application of quantitation is to determine the amount of the active compound present in the sample. Also, it allows you to monitor concentration changes in series.
6.1.2 Working with the Quanalyst dialog box

In this section, we are going to use the same series that we have processed in the previous chapter. 1. Make sure that the Group Treatment mode is on ( ).
2. From the Tools menu, choose Quanalyst to display the corresponding dialog box. 3. To form the quantitation script, in the Quanalyst dialog box, click Insert Quantitation Variable dialog box appears. . The
4. Specify the object and its properties. For the given example, we recommend that in the Object box, you select Peak. Note that in the Property box, Position is set by default. 5. In the Variable box, type P1. 6. In the Description field, you may type any textual string describing the quantitation string. Now the Quantitation Variable dialog box should look like this:
Note
If you select the Keep as Result check box, the result of the quantitation string will be added on the User Data panel.
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7. Click Options. As soon as you do so, the Peak Position dialog box appears. 8. Specify the values as follows:
Depending on the property chosen, the dialog box with the options specific for that property appears. More details on each object and its properties can be found in the ACD/1D NMR Processor and 1D NMR Manager Reference Manual (NMRMOD_R.PDF) located in the ACD/Labs documentation folder (\\DOCS). 9. Click OK. You are returned back to the Quantitation Variable dialog box. 10. Click OK to add the string to the list in the Quanalyst dialog box:
Note
11. Click Insert
once again to specify the next line of the quantitation script.
12.In the Variable box, type Height. In the Object box, select Peak and in the Property box, select AbsHeight. 13.Select the Keep as Result check box. 14. Click Options, and in the Position box, type P1, and then click OK. Therefore, we use the P1 parameter, where we are saving the result of the first string, to define the position of the peak whose absolute height we calculate. 15.You are returned to the Quantitation Variable dialog box, click OK. Note that the second string is added to the list.
Note
When the script is executed, the strings are applied in the order that they appear in the list. Thus, when forming the script, ensure that your strings are arranged in a reasonable order. To move a string up or down, select it, and then click Up or Down correspondingly.
16.Repeat the above steps until all of the desired quantitation strings are listed in the Quanalyst dialog box.
Tip If you have not opened the appropriate file yet, save the assignment by clicking Save
, open the required spectral document, and load the quantitation script by clicking Load .
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17.In the Quanalyst dialog box, click Run
to execute the quantitation script:
To edit the created quantitation script, use the buttons located to the right. Tip Alternatively, you can manage the Quanalyst dialog box using the commands from the shortcut menu (right-click within the script box to display this menu). 18.Click Close to close the Quanalyst dialog box.
6.1.3 Adjusting the Quantitation Graph

The Quantitation Graph command displays resultant responses versus the selected property (user data) and passes data to the Curve processor for regression analysis. 1. From the Tools menu, choose Quantitation Graph; note that the Graph subwindow appears. 2. Right-click within the Graph subwindow to display the shortcut menu, and then choose Select Data to display the corresponding dialog box:
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3. From the Select X Axes drop-down list, choose d2. 4. In the Select Y Axes area, click the User Data box, and then select Height. 5. Click the Style box to display the Curve Style dialog box. Adjust the curve style and color:
6. Click OK to return back to the Select Data dialog box that now should look as follows:
7. Click OK to close it. 8. Right-click within the Graph subwindow, on the shortcut menu that appears, point to Edit, and then choose Title. 9. In the Edit Title dialog box, type Relaxation Curve:
Note
In the same way, you can also edit the name of the Horizontal and Vertical axes.
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10.Click OK to close the dialog box and view the results:
For the series collected from the 1.ESP, 2.ESP, 3.ESP, 4.ESP, and 5.ESP files, the quantitation graph will be different. The size and position of the Graph subwindow can be changed. To move the subwindow, simply drag it with a mouse and place it anywhere you want. To resize the subwindow, drag on the borders of the window. Tip You can manage the Graphic subwindow using the other commands from the shortcut menu (right-click the window to display this menu). 11.From the File menu, choose Close All to close all the files.
Note
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7. Creating Report
7.1 Objectives
This section of the guide provides you with the basics of creating a professional report. You will learn how to: Define the page size and orientation as Landscape or Portrait; Transfer the spectrum to a chemical graphics interface (the ChemSketch window); Modify settings for output of the spectrum; Modify graphic objects within the report; and Create a template-based report. To demonstrate these possibilities, we will use the 1H NMR spectrum of catechin (CATECHIN.ESP) that you can find in the example folder or you can use the same spectrum that we used in the previous sections and saved after processing and analyzing (CATEC_FT.ESP).
7.2 Creating a Standard Report

After you have finished the spectrum processing, you can create the report page. 1. From the File menu, choose Page Setup to display the Page Setup dialog box:
2. Select the Landscape option.
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3. Click the Margins tab and choose the size of borders. Note that the changes are automatically reflected in the preview area on the right side of the dialog box:
4. Click OK. Note that the Poster tab is described later in this chapter. 5. On the General toolbar, click Horizontal Zoom and drag over the area of the spectrum that you want to include in the Report Page to select it.
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7.3 Report Page Setup

You can output the spectral data after processing in a form that can be further used in presentations. Spectral document(s) can be placed to the ChemSketch window, exported to PDF, or printed. But at first the required settings for spectrum report page should be specified. 1. On the Edit menu, point to Create Report, and then choose Standard to display the Report Page Setup dialog box.
Tip ,Alternatively, to display this dialog box, on the General toolbar, click one of the
following buttons
. If any of these buttons are hidden, click the right
white angle of the corresponding template-based report related buttons to display the hidden ones. 2. On the Spectrum tab of the Report Page Setup dialog box, specify whether the whole spectrum, its zoomed-in part, or both are to be included in the report. You can include the calculated spectrum in the report along with the experimental one by selecting the Show Last Calculated Spectrum check box. Here you can also set the units for gridlines and the display mode for series.
Note
If the Show Last Calculated Spectrum check box is unavailable, that means that the program does not see the last calculated spectrum. This can occur, for example, if you have saved a calculated spectrum and then opened it via the Open command on the File menu. If this is the case, to calculate the spectrum once more, from the Tools menu, choose Calculate Spectrum or, on the Analysis menu, point to Assignment, and then choose Verify (for more details, refer to Section 4.10.1). From the Options menu, choose Spectra Calculations to customize options for spectra calculations.
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3. On the Tables tab, choose the tables to be included in the report. You may find some of the options unavailable, which means that the corresponding operations were not performed with the spectrum:
If you select the Multiplets in Journal Format check box, information on the multiplets and coupling constants defined for the spectrum will be placed in the report in the following way: 6.71(d, 1H, J=2.05 Hz) shift value (multiplet type, number of protons, coupling constant value) 4. On the View tab, choose the elements (gridlines, scales, chemical structure) to be present in the report:
Note
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5. On the Text tab, enter any comments or user information:
6. Specify information to be inserted into the report and click OK. You are switched to the ChemSketch window where you can see the report.
7. In the ChemSketch window, on the top General toolbar, click Full Page to view the whole page. This is an exceptionally easy way to view the total page appearance, all at once. 8. Modify the report, if desired, as described in the section that follows.
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7.4 Modifying the Spectrum Report

Once the spectrum is copied to the ChemSketch window, you cannot change spectral modes or settings, although you can change the style, size, and location of the 1D NMR spectrum as a graphical object: To manipulate any graphical object in the report, verify that you are in Draw mode with Select/Move/Resize active. To move the spectrum, text box, or structure, drag the object you wish to move. To resize any object, click the object once to select it, point to one of the small black nodes, and then d rag to resize. To make other modifications, double-click the part of the report you want to edit.
7.4.1 Changing the Spectrum Display

1. Double-click the 1D NMR spectrum image to display the Objects Panel (Spectrum) dialog box:
2. Using this dialog box you can suppress gridlines, change the font of the labels and axes, or change the color and line thickness of the integral lines. 3. On the left of the title bar, click Close Box to close the panel.
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7.4.2 Changing the Table Display

1. Double-click in any table displayed to access the Objects Panel (Table) dialog box:
2. Specify the desired settings to adjust the arrangement of rows, data alignment, style of borders, shading, etc., thus modifying the table display.
7.4.3 Changing the Structure Display

Similarly, double-clicking the structure will display the Objects Panel (Structure):
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7.5 Creating a Poster

A little-known feature of the ChemSketch report interface is that a multi-page poster for displaying your results can be easily created. 1. On the Window Switching bar, click Processor appears, choose Switch to the Spectrum Window. and, from the shortcut menu that
2. In the Processor window, from the File menu, choose Page Setup. 3. In the Page Setup dialog box, set the margins to 30 mm each. 4. Click the Poster tab and choose the integer number of pages so that the right-hand side schematically reflects a large spectrum:
5. Click OK. 6. On the General toolbar, click Copy to Report Editor . In the dialog box that appears, click OK and this will again switch you to the ChemSketch window, with a larger document size sketched in.
7. Modify the positions and sizes as desired, and then, from the File menu, choose Print. 8. Switch back to the Processor window.
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7.6 Creating a Template-Based Report

In addition to standard reports, template-based reports are introduced in each module of ACD/SpecManager. In other words, you can create a report template (which allows you to insert one or several spectra, any table, graph, or any other spectrum related object) in the ChemSketch window, save it into a separate file, and then use this template for reporting. To display the Select Report Template dialog box: On the Edit menu, point to Create Report or to Export Report to PDF, and then choose By Template. On the File menu, point to Print Report, and then choose By Template.
Tip Alternatively, click the corresponding button on the General toolbar
. If
any of these buttons are hidden, click the right white angle of the corresponding standard report related buttons to display the hidden ones.
For more information on creating templates, refer to the ACD/Report Template Tool Reference Manual (REPTEMPL.PDF) located in the ACD/Labs documentation folder (\\DOCS). 1. In the Select Report Template dialog box, click Browse to specify the name and location of an example report template file (1H_EXAM.SK2). The file is likely to be located in your ACD/Labs installation directory in the EXAMPLES\SPECMANAGER\1DNMR folder.
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2. Click OK. The report is instantaneously created and you are transferred to the ChemSketch window. For instructions on editing a report, see Section 7.4.
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8. Macro Processing
8.1 Objectives
All modules of SpecManager include a powerful and flexible feature that allows you to save time and reduce tediumMacro Processing. In this section, you will learn: What a macro and group macro are; How to create a macro; How to edit a macro; and How to process a batch of spectra without opening them using the group macro feature and how to place them automatically into the database.
8.2 What Is a Macro and Group Macro?

A Macro is a set of commands you group together into one single command that will help you with routine tasks. Each macro can be assigned a button or a shortcut key thus allowing you to perform a series of tasks by a single click or keystroke. A Group macro is a macro that can be applied to a whole group of spectra, even if they are not open. Thus, it is a kind of built-in batch processing engine. You can use macros and group macro features for the following purposes: To speed up spectrum processing; To automate complex tasks; To process spectra on the fly as you load them; and To process a batch of spectra and place them into a database without opening them.
8.3 Creating a Macro

There are several ways you can create a macro. Below you will find the description of all possible ways, though you may use any combination of them to create a macro that will be of the most use for you. Open any spectrum you want to process using the instructions below. You may also use any spectrum from the example directory of the ACD/Labs folder.
8.3.1 Macro Organizer

The Macro Organizer is the most effective tool for storing and managing any created or saved macro(s). The Organizer will help you not only to create a macro and give it a meaningful name, but also assign a shortcut to each macro and/or define any macro as auto (i.e., a macro that starts automatically each time you load a spectrum).
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In the Processor window, to display the Macro Organizer dialog box, either click Show Macro on the Macro toolbar or, on the File menu, point to Macro, and then Organizer choose Organizer. If you display it for the first time and have not created any macros yet, it is empty. Before creating a macro, ensure that the type of spectrum is specified correctly in the Type box. For this exercise, it should be set to 1D NMR:
8.3.2 Creating from Template

The easiest way to create a macro is to use a template that contains the most common commands. 1. In the Macro Organizer dialog box, click Template. The dialog box with the most common operations that can be applied to a spectrum appears. 2. Choose the required options by selecting the check boxes and, if necessary, specify options by clicking Options next to the corresponding command (for more details on each command, refer to the ACD/1D NMR Processor & Manager Reference Manual (NMRMOD_R.PDR) located in the ACD/Labs documentation folder (\\DOCS) or use the online Help). 3. As soon as you have selected all of the necessary commands, click OK and the macro is given a name (Macro001, 002, etc.) and is placed into the Macros list.
Note
For more information on how to work with created macros, refer to Section 8.5.
8.3.3 Creating Manually

Sometimes if the commands available in the template are not enough for your work, you can create a macro using the whole list of macro commands. 1. In the Macro Organizer dialog box, click New to display the Edit Macro dialog box:
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2. To form the list of macro commands, click Insert Macro Command available commands arranged in alphabetical order:
to display the list of
3. Double-click the command you want to add. The dialog box with options specific for that command appears. 4. Specify the options and click OK to add the command to the list. For more information on each command, refer to ACD/1D NMR Processor & Manager Reference Manual (NMRMOD_R.PDR) located in the ACD/Labs documentation folder (\\DOCS). 5. Repeat steps from 2 to 4 to form the list of commands.
Important When the macro is running, the commands are applied in the order they
appear in the list. Thus, when forming the macro, ensure that the commands are arranged logically. 6. To change the order of macro commands in the list, click the command you want to move to highlight it, and then click either Move Line Up or Move Line Down .
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7. You can also add any comments. Highlight the line to which you want to insert a comment . In the Edit Comment dialog box, type the text and and click Insert Macro Comment click OK. The comments appear in the list as green lines and are used to specify any additional information that will help you identify the macro:
8. As soon as the macro body is ready, click OK. 9. The dialog box prompting you to save the macro appears. Specify the name and location for the macro file and click OK. The macro is added to the list in the Macro Organizer dialog box.
8.3.4 Creating from History

Another way to create a macro is to process one typical spectrum, and then use the history of its processing as a macro basis. 1. Open the spectrum and process it as usual. For example, process FID, remove solvent, correct baseline, and apply Peak Picking, Integration, and Auto Reference, as described in Chapters 3 and 4. 2. From the View menu, choose History to display the following dialog box:
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3. As you can see, it contains a report on all the actions performed. Note that practically each change in the spectrum is reflected in the history. To make a macro of it, click Macro and the history records are automatically converted into macro commands and placed into the Edit Macro dialog box:
4. To save the macro, click Save Macro
8.3.5 Creating via Quanalyst

There is also a possibility for converting a quantitation script into a macro (see Section 6). A quantitation script works actually on a pretty similar basis as a macro, though the former is easier to handle. However, the range of actions you can perform using macro commands is much broader than those allowed by Quanalyst.
8.3.6 Settings for Macro Execution

The process of macro execution, can be customized using the Macro Settings dialog box: 1. On the File menu, point to Macro, and then choose Settings.
Tip Alternatively, to display this dialog box, click Settings
in the Macro
Organizer dialog box.
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2. In the Macro Settings dialog box that appears, specify your preferences on the program behavior concerning macros execution. You can set the following options in this dialog box: To
Skip entering manual mode
Do this
Clear the Apply Manual Modes check box. If you keep it selected, each time the macro reaches the EnterManualMode command the selected mode will be enabled and the macro execution will be paused until you continue with the macro processing. Select the Step by Step check box. Select the corresponding option in the Action on Error area: Quit Macromacro will be exited. Pause Macromacro will be paused until you either continue it or quit manually. Ignoreerror will be ignored and the macro will be continued. Set the corresponding options in the Show area.
Stop at each step of macro running Control errors appearing in the process of macro running
Show/hide macro protocol and macro processing status box
Note Other options of the Macro Settings dialog box are described later in the chapter. 3. Click OK to apply the specified settings and close the dialog box.
8.4 Editing a Macro

The commands and comments available in a macro can be modified via the Edit Macro dialog box. to display the Macro Organizer dialog 1. On the Macro toolbar, click Organizer box. Make sure that the type of spectrum is specified correctly (1D NMR). 2. Click the macro you want to edit in the list and click Edit to display the dialog box with the macro contents:
Note
If you have not added your macro to the organizer, you can edit it by loading it into this dialog box directly. On the File menu, point to Macro, and then choose Edit. Click Load Macro . Alternatively you can choose Organizer, and then click Add. Then find the required macro file.
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3. To edit any command, double-click it or select it, and then click Edit Current Line
For more detailed information on the buttons from the Top toolbar that you can use to modify macro, refer to the ACD/1D NMR Processor & Manager Reference Manual (NMRMOD_R.DOC located in the ACD/Labs documentation folder (\\DOCS).
8.5 Managing Macros

You can perform the following operations that can help your macros to be executed and managed in the most appropriate way: Place the most frequently used macros on the toolbar as buttons with distinctive names and a comprehensive hint for each of them. Create a shortcut key for any macro. Define any macro as auto so that it is automatically started each time you load a spectrum. Set the log file for automatic storing of macro processing results. For more information on each of the points above, refer to the sections that follow.
8.5.1 Placing Macros as Buttons on the Toolbar

1. On the File menu, point to Macro, and then choose Show Macro Bar. 2. From the File menu, open the Macro Organizer dialog box and, in the list of macros, click the boxes next to the macros that are to be placed on the Macro bar to select them with blue check marks. 3. If necessary, for each macro, enter a distinctive name for the button (Name box) and comment (Hint box) that will appear as a yellow hint when you point to the macro button on the Macro toolbar. 4. Click OK and the selected macros will be added to the toolbar right below the Operation toolbar.
8.5.2 Setting a Shortcut Key for Macro Execution

1. On the File menu, point to Macro, and then choose Organizer to open the Macro Organizer dialog box. 2. In the list of macros, highlight the macro for which you want to set the shortcut. 3. From the Shortcut drop-down list at the bottom of the dialog box, choose the number or character for the shortcut, and then click Assign. For example, if you set M, pressing SHIFT+M will start the corresponding macro. 4. Click OK to save changes you have made and close the Macro Organizer dialog box.
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8.5.3 Autorunning a Macro upon Spectrum Loading

1. Open the Macro Organizer dialog box and click Settings .
2. In the Macro Settings dialog box, in the Auto Run After area, select when the macro defined as auto should be activated: on spectra opening, importing, or/and loading from a database. 3. Click OK to close the dialog box and apply the settings. 4. In the Macro Organizer dialog box, highlight the macro you want to set as auto, and then select the Auto Run check box. Click OK. From this point on, this macro will be applied each time you open, import, and/or load a spectrum from a database (depending on the selected option(s)).
8.5.4 Logging Macro Processing Results into a File

1. On the File menu, point to Macro, and then choose Settings Macro Settings dialog box. 2. Select the Save Protocol check box. In the File Name box, click Browse to display the .
3. In the Select File dialog box that appears, specify name and location of the file that will be used for data logging, and click Save. 4. Click OK to close the Macro Settings dialog box. From this point on, all of the macro processing results will be written to the specified text file.
8.6 Processing a Group of Spectra (Group Macro)

The Execute Group Macro feature provides you with another very convenient option. If you want to apply the same set of commands to several spectra, you dont need to open the spectra one by one. You just have to specify their names and the name of the macro to be applied. The macro commands will be automatically applied to the files and the results will be saved, placed into a database, or treated otherwise. Note that this option can process up to 16,000 spectra. In the Processor window, on the File menu, point to Execute Group Macro, and then choose 1D NMR to display the Execute Group Macro dialog box. This dialog box contains three main areas: the Spectra area (for the list of spectra to be processed); the Structures area (for the list of structures to be attached to the spectra; this field is optional); and the SDF Record area (for assigning each structure a specific value). The following steps are based on the example file, M96.ND9 that can be found in the EXAMPLES\NMRPLATE directory of the ACD/Labs folder (by default this is ACD12\EXAMPLES\NMRPLATE). It contains 96 FIDs of samples from a combinatorial plate.
8.6.1 Specifying Plate Type

A feature in the Group Macro engine is the ability to define what plate type should be used when processed spectra are placed into a database. 1. To enable the Plate mode, select the Plate check box, and then click Configure to display the Plate Configuration dialog box.
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2. In this dialog box, you can configure the plate where spectra will be placed after processing. If you are going to use the example files mentioned above, set the configuration as displayed below:
3. Click OK to apply the changes and close the dialog box. 4. In the Name box under Plate, enter the name for the plate, for example, 1-96. This name will be used when spectra are placed into the Plate subwindow of the Database Window.
Tip To add spectra to a specific plate of the database, you should correctly specify its
name; otherwise a new plate will be created.
8.6.2 Specifying a Group of Spectra

Now we can specify the spectra to be processed and placed into the database. 1. In the Changes in List area, ensure that the options are selected as follows:
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2. Click Add Group to display the Add Group of Spectra dialog box where you should specify the directory and File Mask of the required files. In our case, the directory mask will look something like the following: C:\ACD\EXAMPLES\NMRPLATE\SPECTRA\*02_???
Important If you are adding spectral files in the Plate mode, then the asterisk character
"*" should be present in the mask. It will be interpreted by the program as the spectrum number and will be used for sorting files in accordance with the set Plate type. The question mark "?" should be used to replace characters that are different in the folder or file names. In our case, files are organized in the following way: \0102_AMS\ \0202_AMW\ ... \9602_AIW\ As you can see, each directory name contains different characters. So in the directory mask: *02_??? asterisk * will be interpreted as the spectrum number (from 1 to 96) and the question marks stand for last two characters that are different in each folder name. Note If the Plate mode is disabled, asterisks and question marks are interpreted as usual masks: * stands for any set of characters and ? for one character. 3. As you click OK, the list of files is updated to the Spectra column:
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8.6.3 Specifying Processing Options

1. Now you should specify the processing options that will be applied to the spectra. In the Macro Name area, click Select Macro . 2. In the Macro Organizer dialog box that appears, you should choose (or create) a macro to be applied to the spectra. For more information on creating and managing macros, refer to Section 8.3 of this tutorial.
Important When creating a macro for group processing, make sure that it includes at
least one of the macro commands allowing you to save, export, report, or add the obtained results to a database (e.g., CopyToSketch, CopyToWindow, DatabaseLists, Execute, ExecuteChemBasicApp, ExportDocument, ExportReportToPDF, ExportTable, Print, SaveDocument, or UpdateCurrentDatabase)otherwise the results will be lost. For the current example, in the Macro Organizer, click Add and find the M96.MCR file in the EXAMPLES\NMRPLATE directory of your ACD/Labs folder. It was specially created for processing the provided files. If you wish, you might view the commands it contains by double-clicking the macro name in the list of macros. If you do not want to use this macro, and are going to use your own, please ensure that it contains UpdateCurrentDatabase as the last command. 3. In the Macro Organizer dialog box, click OK to place the macro name into the Macro Name box:
8.6.4 Attaching Structures to Spectra

Now you can specify the structures that will be automatically attached to the specified spectra. You can either attach each structure one by one to each spectrum or you can add a whole group of structures at once, if the structures have been saved in the MOL or SDF format. In the Changes in List area, select the Structures option:
8.6.4.1 One by One

To attach a structure from either an MDL molfile or SDfile to a specific spectrum, highlight the required spectrum file in the list and click Add. This brings up the Attach structure(s) from dialog box where you can find the file to be attached. In our exercise, we will not consider this option.
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8.6.4.2 Group of MDL Molfiles

We include this section just to demonstrate you how attach MDL molfiles, but it is not based on any particular example. 1. To add a group of files at a time, click Add Group. The Add Group of Structures dialog box appears:
2. Choose the MDL molfiles option, and then click Options, to specify the location of the directory where the molfiles are located. 3. In the Add Group of Structures dialog box, click OK to attach all of the MDL molfiles from the specified directory to the spectra set in the list in succession.
Tip You can change the position of an MDL molfile or spectrum (depending on the option
selected in the Change in List area) in the list. Click the corresponding row and use the Up or Down arrows to move the current spectral or structure file.
8.6.4.3 Group from an SDfile

Note that this option is considered in our example. 1. To add structures from an SDfile, click Add Group, and select the MDL SDFfile option:
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2. Click Options to display the dialog box in which you can specify the name of the SDfile that will provide the structures. In the example directory, you may find the SDfile containing structures matching the spectra you have set in the Spectra list. The path will be something like in the screen shot:
3. In the Key Field box, you should enter the name of the SDfile field that will coordinate the structures with the spectra. For example, lets say that you have input "ACD_ID" fields in your SDfile and in the next string you have set the ID number of the record to which each structure should be attached: > <ACD_ID> B1 Then if you type ACD_ID in the Key Field box, all of the structures identified by that field in the SDfile will be attached in accordance with the set numbers. For the current example, type PLATE in this field. If you leave the Key Field box empty, structures from the specified SDfile will be attached to each database record as they appear in the file in succession. If the Include Structure Attributes check box is selected, any additional information available in the SDfile will be added to the database as the spectrum or structure user data. 4. After you have set the required file, click OK. The specified file is placed into the list:
Note
5. In the Structure Preview area, the structure currently highlighted in the list is displayed. If this is not the structure you want to be attached to the corresponding spectrum, you can enter the key field and value of the required structure from the current SDfile to the corresponding boxes of the SDF Record area, and then click Update. The program finds the specified structure and displays it in the field.
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8.6.5 Executing Group Macro

After all the required parameters and spectra to be processed by group macro are specified, it is time to start processing. 1. In the Execute Group Macro dialog box, click OK. The Group Macro Processing panel appears:
Note You can stop the process at any time by clicking Cancel. 2. If you have previously selected the Pause Macro option in the Action on Error area (Macro Settings dialog box) and an error occurs during the macro processing, the program stops the macro execution and displays the error message. For example, if you havent open any database before starting the group macro processing, and if the macro includes the UpdateCurrentDatabase command, the program prompts you to open a database before proceeding:
3. On the Window Switching bar, click Database and open any existing database or create a new one. by clicking Processor
to switch to the Database window
4. As soon as the database has been created and opened, switch back to the Processor window on the Window Switching bar.
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5. In the Processor window, on the upper General toolbar, you can see additional buttons appear which allow you to control the macro processing: continues macro processing; skips current document (file to be processed); and stops macro processing. Click Continue Macro Processing to proceed with the process. 6. After the process is finished, the program displays the Macro Protocol containing the paths and names of the original files, the list of commands applied, and the paths and names of the resulting files. Any read or write errors will be flagged as well.
7. To verify that the database is properly created, switch back to the Database window, and then, on the View menu, point to Screen Forms, and then choose Plate.
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8. From the Plates menu, choose Indexed Wells to display the records assigned to plates in accordance with the settings you have set:
8.7 Applying Intelligent Bucketing to Thousands of Spectra

ACD/1D NMR Manager allows you to create the Table of Common Integrals for a series including up to several thousands of spectra. This allows processing of a metabonomics measurement of any size. 1. On the File menu, point to the Execute Group Macro, and then choose 1D NMR. 2. In the Execute Group Macro dialog box that appears, specify the spectral files you want to be processed. 3. Click Select Macro and, in the Macro Organizer dialog box that appears, click New .
4. In the Edit Macro dialog box that appears, create the macro which will create the temporary spectrum of sum or projection and apply the intelligent bucketing to it.
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For example, the following macro: CheckValue (Value = "$(DOCNUMBER)"; Pattern = "1"; Condition = "Equal"; UseCase = False; Group = "") Execute (Application = ">rm"; Parameters = "$(TEMPDIR)\projspec.esp"; Mode = "Wait"; Hidden = True) CheckEnd (Group = "") ProjectionSpectrum (FileName = "$(TEMPDIR)\projspec.esp") CheckValue (Value = "$(DOCNUMBER)"; Pattern = "$(DOCCOUNT)"; Condition = "Equal"; UseCase = False; Group = "") IntelligentBucketing (Width = 0.04; WidthLooseness = 50; Method = "Projection"; RefValue = 1; RefType = "WholeSpectrum") CheckEnd (Group = "") SaveDocument (Dir = "$(TEMPDIR)"; FileName = "projspec.esp"; IfExist = "Overwrite") 5. After the macro is created, save it to an .MCR file. Click OK and, in the Save Macro File As dialog box, specify the name and location for the file. 6. Note that the macro is placed into the Macros box of the Macro Organizer dialog box and its name is displayed in the Name box. 7. Click OK to insert this macro in the Execute Group Macro dialog box. Since the spectral files and macro are specified, click OK to start group macro processing. As a result of the macro execution, the created integral ranges are saved into the file, and now we can apply them to all the spectral documents present in the Execute Group Macro dialog box. 8. Repeat steps from 1 to 3 to proceed with a new macro which reads the integral ranges (buckets) in the temporary file and creates the integrals on the same positions in all of the source spectra. EXAMPLE: Integration (Method = "UseIntervalsFromFile"; RefValue = 1; RefType = "AllIntegrals"; FileName = "$(TEMPDIR)\projspec.esp") ExportTable (Table = "Integrals"; Dir = "$(TEMPDIR)"; FileName = "integrals.txt"; IfExist = "Overwrite") SetVariable (Name = INTFILE; Value = "$(TEMPDIR)\integrals.txt") SetVariable (Name = resfile; Value = "$(TEMPDIR)\resfile.xls") SetVariable (Name = column; Value = "non-negative value") ExecuteScript (Script = "$(MACRODIR)\collect_integrals.pas") 9. After the macro is created, repeat steps from 5 to 7 to save it and apply to the specified spectral files. As a result of this macro execution, the obtained Table of Common Integrals is exported into the INTEGRALS.TXT file and the Pascal script (collect_integrals.pas) displays this table in Microsoft Excel.
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9. Integrating Experiment and Prediction

9.1 Objectives
ACD/1D NMR Manager is fully integrated with ACD/C+H NMR Predictors and DB. This integration means that the .NMRUDB, HUD, or CUD database files that are created in the ACD/C+H NMR Predictors and DB program can now be automatically updated with peaks of the spectrum processed by 1D NMR Manager. In this chapter, you will learn how to set up the automatic transmission of peak data from NMR Manager to CHNMR Predictors. Although it will not be described explicitly, this is also the method to be used for XNMR spectra.
9.2 Preparing an Experimental Spectrum

Important Before updating the database:
You should assign the atoms of the structure to peaks in the spectrum. In Chapter 4, there is a detailed description of the process of peak assignment for the catechin molecule; and The C+H NMR prediction software should have been installed to the same directory as 1D NMR Manager. After completing Chapter 4, (Section 4.10, Assigning Peaks and Verifying the Structure), you should have the catechin structure with assigned peaks that looks approximately as follows:
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9.3 Preparing Predictor Database

1. From the ACD/Labs menu (which lists the ACD/Labs software installed to the same folder as 1D NMR Manager), choose C+H NMR Predictors and DB:
If C+H NMR Predictors and DB is not available as a choice on this menu, minimize the window and locate the program CHNMRPRO.EXE within the \\ACD12 directory and start it up directly by double-clicking. 2. You will see ACD/C+H NMR Predictors and DB being loaded, and then you will be placed in the ChemSketch window. to switch to the Database window. 3. On the Window Switching bar, click Database If you havent opened a database in ACD/C+H NMR Predictors and DB and there is no default database specified in the Default Directory and Database dialog box (from the Options menu in the Database window, choose Default Directory and Database), an empty Database window appears in this case.
Note
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4. Open the database (click Open User Database ) you want to update or create a new one (from the Database menu, choose New). Make sure that you are in the Update mode (the Switch User Database to Update Mode button should be pressed in ).
9.4 Transferring Chemical Shifts

1. From the ACD/Labs menu, choose SpecManager to switch to the Processor window of SpecManager. 2. In the Processor window, from the Database menu, choose Update C/H NMR Database. The Not Assigned Peaks dialog box appears containing a list of unassigned peaks that will not be automatically placed into the database:
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3. Select the Included check boxes in the table displayed to define the unassigned peaks you want to be included.
Important It is highly recommended not to update peaks of impurities and solvents into
the C+H NMR databases since they may cause wrong predictions. 4. As soon as all of the required peaks are defined in the list, click OK. The database currently opened in the Database window of ACD/C+H NMR Predictors and DB will be updated.
Note
If the database you update already contains the same structure, it will be updated with new chemical shifts.
5. On the Window Switching bar, click Back to SpecManager back to the Processor window.
to go
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9.5 Using a Database to Calculate a Spectrum

You can use created .HUD, .CUD, and .NMRUDB databases for calculating theoretical spectra in ACD/SpecManager. 1. To specify the database to be used for calculations, in the Processor window, from the Options menu, choose Spectra Calculations to display the Calculation Options dialog box. For more information on options available in this dialog box, refer to the ACD/1D NMR Processor & Manager Reference Manual (NMRMOD_R.PDF) located in the ACD/Labs documentation folder (\\DOCS).
2. Select the Use Training Database(s) check box, and click Browse
3. In the System Training Options dialog box that appears, specify the database(s) whose data should be used for calculation of theoretical spectra, and then click OK. If the Use Training Database(s) box is left empty, a standard predictor database is used. The specified database(s) will be taken into account when the Auto Assignment feature is used and when the program calculates a spectrum for the structure (from the View menu, choose Calculated Spectrum). Specified database(s) will be also updated automatically during execution of the Update C/H NMR Database command if there is no database currently open in ACD/C+H NMR Predictors and DB respectively. For more details on how to work with C+H NMR databases, refer to the ACD/C+H NMR Predictors and DB Tutorial (CHNMR_T.PDF) located in the ACD/Labs documentation folder (\\DOCS).
Note
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Appendix. How To
Objectives
In this chapter you will find some general instructions on how to perform most common operations in ACD/1D NMR Manager. Note that the sections below are not based on any particular examples.
Register User Formats

In addition to the major file formats mentioned in the ACD/1D NMR Processor & Manager Reference Manual, ACD/SpecManager allows you to register any other user format so that the software can recognize it. The only thing required is the external converter program that can import from and/or export into JCAMP, ASCII, Galactic, or ACD/Labs formats in the commandline mode. The general scheme of the conversion is as follows. For example, you have a program that can convert from any external format (not supported by 1D NMR Manager) into the ASCII format. So, to be able to make SpecManager read your files, you specify the .EXE file of your converter, the key (the command line you use for exporting into different formats), and that your converter understands ASCII format. When you import a file using the external format into SpecManager, it starts your converter and makes it export that file into ASCII format, then takes the resultant file of ASCII format and imports it into SpecManager. The result is that you can open and process your file in SpecManager.
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Following a similar pattern, you can register your converter to be used for exporting back into your format (only if your converter can import into one of the mentioned above formats). 1. From the File menu, choose Register User Formats to display the Register User Formats dialog box:
2. First, go to the Filter Location box and specify the directory and name of the converter. 3. In the Filter Name box, enter the name of the filter as it will appear (with a tilde (~) sign before it) in the Import and/or Export dialog boxes in the list of supported formats. 4. From the Doc Type list, select the type of spectrum supported by the filter (1D NMR). 5. In the File Extension box, specify the extension of the file format you are going to import or export. Note that if the format uses several file extensions, you may use the wildcard characters (*.*) to define it. 6. Select the Import check box if you intend to import files using the converter. In the Key field, specify the command-line string that is used by the conversion program to export files (for more details, refer to the online Help file of the converter you use). Note that you should use the %I argument for defining the input file and the %O argument for the output file. 7. In the Output Format list, select the format into which your conversion program can export files. 8. Select the Export check box if you intend to export files using your conversion program. In the Key field, specify the command-line string that is used by your converter to import files. 9. In the Input Format list, select the format from which your conversion program can import files. 10.If everything is specified correctly, the Add button becomes active. Click it to place the filter into the list. 11. Click OK.
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Import from an ASCII File

1. From the File menu, choose Import to display the corresponding dialog box. 2. In the Files of type list, select ASCII (.TXT) and find the file you want to import. 3. Click Open to start with the first step of the import operation. 4. In the Import from ASCII File (step 1) dialog box, specify which rows should be imported and choose the decimal delimiter used in the imported file. If necessary, set the specified settings as default. 5. Click Next to proceed to step 2.
6. In the Import from ASCII File (step 2) dialog box, choose the type of the imported spectrum in the Spectrum Type box and designate axes for each data column. To do that, choose the required axis in the Selector field, and then click the header of the data column to set the chosen designation on it. 7. Click Next to go to the final step.
8. In the Import from ASCII File (step 3) dialog box, specify the type, comment, frequency, solvent, and nucleus type to be placed into the Parameters panel relating to the current spectrum, as well as X-units. If there is no data for the X-axis in the imported file and if you have not selected X in step 2, create an X-axis by specifying the offset and step for the Xcoordinates.
Note
If necessary, you can return to the previous step by clicking Previous and the spectrum will
9. As soon as you are ready with all the settings, click Finish be imported.
Shift FID Spectra

Occasionally the experimental free induction decay (FID) data might need to have some of its beginning points cut off (left shifted), or some of its final points removed (right shifted) or you may want to shift a spectrum so that the final points are cut off and placed at the beginning of the spectrum or vice versa (cyclical shift). 1. Make sure that the FID you are going to process is active, and on the status bar, click the . Points button 2. Estimate the size of shift you have to do, using any Zoom tool, if needed. 3. On the Operation toolbar, click Interactive FT . to unfold the
4. In the Fourier Transform dialog box that appears, click FID Shift area where you can specify the required settings for shifting the FID.
5. Select the FID Shift check box and, in the box to the right, specify the number of points by which the FID will be shifted. For example:
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As the Instant Preview check box is selected, the specified settings are immediately reflected on the spectrum plot and will result in the following change (the example below would not likely appear in practice, it is just to demonstrate the way this option works):
Note
If on second thought, you decide that the applied shift is too extreme, edit the number of points until the required result is obtained.
Apply Interactive Apodization

ACD/1D NMR Manager presents you with a very handy feature: Interactive Apodization. This mode allows you to interactively apply the following options: Fourier Transform and Phase Correction. This feature permits an interactive and quick adjustment of the Linear Prediction Parameters, Window Functions, and phase correction parameters for your spectrum. After the required Zero Filling is set for the current FID spectrum: to enter this mode. If 1. On the Operation toolbar, click Interactive Apodization this is the first time you are entering the Apodization mode, you should see the following toolbar:
2. If you have already entered this mode and have any of the buttons pressed, release the Mouse Phasing, Apply Phase Correction, and/or Apply FT buttons before proceeding. and, in the dialog box that appears, specify 3. Click Window Functions Options parameters for applying weighting function to the FID. Click OK. (For more details on the types of Window Functions available in this dialog box, refer to the ACD/1D NMR Processor & Manager Reference Manual, Section 3.6.2.1.)
Note
Depending on the window function you set, one or two text input fields may appear on the toolbar allowing you to specify parameters. You can either type the values manually or drag over the workspace with the left mouse button (changes the LB or n value) or with the right one (changes the GF value) until you achieve the desired results.
4. Click Apply Fourier Transform and the default Fourier transform will be applied to the spectrum. Note that the button remains pressed in and Apply Phase Correction becomes active. to apply phase parameters (Ph0 and Ph1) used in 5. Click Apply Phase Correction the last saved working session. If you are performing phase corrections for the first time, the parameter values will be set to zero.
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Now you can adjust the phase using the Mouse Phasing tool. . , and adjust the phase manually by dragging over 6. Click Phasing with Mouse the spectrum with the right or left mouse button. To leave the Mouse Phasing mode, click the button again to release it. Note that releasing buttons will cancel their actions. to display the 7. On the Interactive Apodization toolbar, click Linear Prediction Linear Prediction Parameters dialog box. Specify the required parameters, and then click Apply. To leave the Linear Prediction mode, release the button. 8. As soon as you obtain the desired spectrum by trying various window functions and phase correction parameters, click Accept Changes
Note
Even if you have left the Apodization mode by canceling the changes made to the spectrum ( ), the parameters you have set will be applied to a spectrum each time you enter this mode.
Manipulate Windows
There are two ways to display several spectral subwindows in the workspace: either tiled (the subwindows are located one under another, so that you can see several of them at once) or full view (each spectral subwindow is spread along the workspace overlaying each other; the active being on top). Choose among them by clicking the corresponding or Full . You can also set the number of tiled spectral subwindows buttons: Tile to be displayed in the workspace at a time by using the Set Scrolling command (Windows menu). If there are several subwindows open in the Processor window, one of them is active. The tab of the active subwindow is dark-blue in color (if the Tile mode is on) or marked with bold (if the Full mode is on). To make a subwindow active, open the Table of Windows (from the Windows menu, choose Table of Windows). In the table, double-click a row corresponding to the spectrum you need to make active or highlight this row and press ENTER. Text captions of the subwindow tab can be changed in the Set Caption dialog box (Windows menu). To change the order of the subwindows in the workspace, you can move them. Make the subwindow you want to move active, and then drag its tab up/down (if the Tile mode is on) or left/right (if the Full mode is on) to locate it where you want; you'll see the cursor or / changes to subwindow to its destination. / . Release the mouse button to move the
To be able to work with several spectral documents at a time, you should first select the corresponding subwindows. To select/deselect several subwindows at a time, click the subwindow tabs while holding down SHIFT. The tabs of the selected subwindows are light-blue. The active subwindow is also considered selected and participates in multispectral operations. Having several spectra selected will allow you to apply some of the operations (Synchronize and Arithmetic options) to all of them.
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Enlarge Spectrum View

Very often in your work, you will need to enlarge a spectrum region to have a better view of its peaks. ACD/SpecManager presents a set of tools which allow you to zoom in any spectrum portion in the way most suitable for your needs: Using the Horizontal Zoom tool or Rectangular Zoom tool
Both tools have the same principle of operation The tools differ in that the rectangular zoom will magnify the y-axis as well as the x-axis. Click either of these buttons, and then drag over the spectral region you want to enlarge. The working area is split into two areas. The Spectrum Display area now displays the enlarged region view; the Zoom Area panel displays the entire non-expanded spectrum with the shaded area denoting the enlarged region. To hide/display the Zoom Area panel, from the View menu, choose Zoom Area. To see the details in different sections of the spectrum, drag or resize the shaded area of the spectrum in the Zoom Area panel. You can also enlarge or reduce the spectrum view in the vertical direction, using either the Vertical Zoom commands or the PAGE UP and PAGE DOWN keys on the keyboard. By manually specifying the coordinates of the area to be enlarged On the View menu, point to Zoom In, and then choose Manual or, on the General toolbar, click . In the dialog box that appears, enter the coordinates of the area you want to Manual Zoom enlarge and click OK. Returning to the normal view To cancel the Zoom In mode and to get back to the full spectrum view, on the General toolbar, . To cancel the steps of Zooming one by one, from the View click Show Whole Spectrum menu, choose Zoom Undo. To reverse the Zoom Undo action, choose Zoom Redo. Keyboard Shortcuts and Miscellaneous Notes Right-clicking in the spectrum area enables the Horizontal Zoom tool. Right-clicking in the spectrum area while holding down CTRL enables the Rectangular Zoom tool, if the Zoom in check box is selected on the Mouse tab of the Common Preferences dialog box. Otherwise, right-clicking triggers the display of the shortcut menu. If you click the spectrum with the Horizontal Zoom tool active, the spectrum will be enlarged three times around the point you have clicked. If you hold down CTRL when dragging with either the Horizontal or Rectangular tool active, the area is zoomed in symmetrically around the starting point.
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Appendix. How To
Lock a Display Range

For applying a predefined zoom to all spectral documents of the same data type on loading them, specify the required coordinates in the Lock Display Range dialog box: 1. From the Options menu, choose Lock Display Range. 2. In the dialog box that appears, select the corresponding check boxes to define whether horizontal, vertical or both types of zoom are to be applied to the spectral documents. 3. In the neighboring boxes, specify the coordinates of the area to be enlarged. Note that once the lock display range parameters are specified, the spectral region will be magnified in all the subsequently opened spectral documents of the same type.
Note
To set the coordinates of the currently enlarged spectral area in the boxes, click
Get Current Zoom . To set the current settings as default or restore the previous default settings, click the corresponding button. 4. To close the Lock Display Range dialog box without saving the changes, click Cancel. If you have previously specified the zoomed region but you want to display the newly opened spectral document as is, on the General toolbar, release Lock Display Range On/Off .
Save Spectral Region as an Individual Spectrum

1. From the Process menu, choose Edit Spectrum to display a new toolbar. and drag over the portion of the spectrum you want to 2. Click Select Region save. As you release the mouse button, the Select Region Operation dialog box appears. 3. Adjust the coordinates of the selected region if necessary, and then select the Cut Off Region option. 4. Click OK and the selected region will be cut off from the spectrum and fitted into the workspace. 5. Save the spectrum using the Save As or Save command from the File menu.
Edit a Spectrum
1. Zoom in the region that you want to edit by clicking Horizontal Zoom the region. 2. From the Process menu, choose Edit Spectrum. is active on the Edit Spectrum toolbar. To edit a 3. Note that Select Region spectrum region, drag over the region of interest. 4. In the Select Region Operation dialog box that appears, adjust the coordinates of the region, if necessary. Select the Set to Constant option, set the height for the selected region, and then click OK.
Note
and dragging over
To cancel all the changes you have made in this mode, click Clear Changes . .
5. To save the changes made and quit this mode, click Accept Changes
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Appendix. How To
Update Spectrum User Data via Data Form

The program allows you to assign a data form to the active spectral document, and then update document user data through it. To assign a form to the spectrum: 1. Make sure that the required spectrum is active. 2. On the Edit menu, point to User Data, and then choose Form Settings. OR Right-click within the User Data panel (to display it, from the View menu, choose Spectrum User Data), and then from the shortcut menu that appears, choose Form Settings. 3. In the Form Settings dialog box that appears, select the desired data form, and click OK. For more information on how to create the user data forms, refer to the ACD/Forms Manager Users Guide located in the ACD/Labs documentation folder, \\DOCS\FORMSMAN.PDF. To input or edit the spectral user data via the assigned form: 1. On the Edit menu, point to User Data, and then choose Data Form. OR Right-click within the User Data panel and, from the shortcut menu that appears, choose Data Form. 2. Fill in the user data form that appears, and click OK. The input user data will be available from the User Data panel (for more information on the panel, refer to ACD/1D NMR Processor & Manager Reference Manual located in the ACD/Labs documentation folder, \\DOCS\NMRMOD_R.PDF.
Note
Update Structure User Data via Data Form

The program allows you to assign data forms to the molecular structure attached to the active spectral document, and then update structure user data through it. To assign a form to the structure: 1. Make sure that the required spectrum is active and the structure is attached. 2. From the View menu, choose Structure User Data. 3. Right-click within the Structure User Data panel and, from the shortcut menu that appears, choose Form Settings 4. In the Form Settings dialog box that appears, select the desired data form, and click OK. For more information on how to create the data forms, refer to the ACD/Forms Manager Users Guide located in the ACD/Labs documentation folder, \\DOCS\FORMSMAN.PDF. To input or edit the structure user data via the assigned form: 1. Right-click within the Structure User Data panel and, from the shortcut menu that appears, choose Data Form. 2. Fill in the user data form that appears, and click OK. The input user data will be added to the Structure User Data panel.
Tip In exactly the same way, you can assign a data form to the Record User Data Note
subwindow, and then insert or update corresponding values via that form.
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Select a View Mode for Selected Spectra

ACD/1D NMR Manager allows you to adjust the representation (view) mode for spectra in a series or for several selected spectra. To switch between the Absolute (AI) and Normalized (Nl) view mode, use the corresponding buttons in the right part of the status bar: or on the View menu, point to Display Mode, and then select the required one. When you select several spectra: The mode does not change if it is the same for all of the selected windows; The mode indicators (Nl and Al) are depressed if the mode is not the same for the selected windows. The spectra representation is not modified until you click one of the buttons to select the desired mode. Maximum peak height in the selected spectra depends on the Vertical Scale Factor or VSF: If the Nl mode is activated, maximum peaksone in each spectrum in the series (in each of the selected spectra)acquire the same height. If the Al mode is activated, the maximum peak among all peaks in spectra in the series (in the selected spectra) acquires VSF*def (def=100) and the heights of maximum peaks in the rest of the spectra are calculated according to the following formula: h(i)=VSF*def*(H(i)/Hmax), where Hmax is an absolute height of the maximum peak, and H(i) is an absolute height of the maximum peak in an i-spectrum.
Search in Databases. General Notes

You can perform searches: Within ACD/NMR databases (from the Database menu, choose Search NMR Database); Within ACD/SpecManager databases (from the Database menu, choose Search Subspectra); From the ChemSketch window by structure or substructure (Search
Note
).
You can perform the above-mentioned searches if ACD/SpecDB and ACD/C+H NMR Predictors and DB are included into your version of ACD/SpecManager. There are two types of searches in the Database window: SingleThe search is performed within the active list (List A) of the open database. MultipleThe search is simultaneously performed within all the databases specified in the Multiple Databases Search dialog box. To include the current database into the search processes, you should also add it to the List of Databases. You can view what mode is currently active (Single or Multiple) on the status bar of the Database window. To switch between modes, simply click that toggle. If you search within the currently open database (Single search), searches are performed through the currently active list of records (List A). Once a search has been made, a subsequent query will search only the list generated by the previous search. For example, if your database contains 200 records and following your first search, the bottom status bar displays ID: 1 of 74, then the next search will be made through the active list of 74 records. To go back and search through the entire database, refresh the active list by clicking Retrieve All Records .
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If you perform a Multiple search, make sure that the Multiple DBs list contains the required databases and the Multiple DBs notice is available on the status bar of the Database window. Before making a Single search, make sure that the database to be searched is open in the Database window and that all of the necessary records are placed into the active list (List A). After you have performed A Single search, the found hits are placed into the active list A. A Multiple search, the program either displays the dialog box with the results of search or opens a new temporary database with the merged found records (if the Auto Merge Search Results check box had been selected in the Multiple Databases Search dialog box).. To obtain the desired result, different types of searches can be combined: spectral, structural, and textual.
Search Shifts in NMR Predictor Databases

ACD/SpecManager is fully integrated with ACD/C+H NMR Predictors and DB. This integration means that the .NMRUDB, .HUD, or .CUD database files which are created in the C+H NMR Predictors and DB program can now be searched for the assigned shifts of the spectrum processed by 1D NMR Manager. NOTE! Before performing a search: Atoms of the structure should be assigned to peaks in the spectrum, or at least spectrum peaks should be labeled; ACD/C+H NMR Predictors and DB should be installed in the same directory as ACD/SpecManager. The preceding section (How to Search in Databases. General Notes) is recommended to be studied. To search shifts: 1. In the Processor window, open/import the spectrum that you want to use for searching. Make sure that the spectrum peaks are labeled. 2. From the Database menu, choose Search NMR Database. ACD/C+H NMR Predictors and DB is automatically loaded and the Open Database dialog box is displayed. 3. Specify the database within which you want to perform a search, and click Open ACD/SpecManager searches according to the parameters (Single or Multiple search and databases to be searched through) which were set in the last working session. So it is better to open ACD/C+H NMR Predictors and DB on your own and make sure that the settings are specified properly. 4. In the Search by Chemical Shifts dialog box that appears, adjust the shift values to be searched, and then click OK. After the search is completed, the program displays the search results and you are switched to the Database window of ACD/C+H NMR Predictors and DB.
Note
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Appendix. How To
Perform Peak, Mixture, Multiplet, and Similarity Searches

Using this feature you can find the spectra containing all of the peaks from the selected area or the spectra entirely identical to the query one. Before performing a search, refer to the How to Search in Databases. General Notes section. 1. Make sure that the required database is open or the Multiple search mode is on. Otherwise, the warning will be displayed asking you to do so prior to continue your work. 2. In the Processor window, switch to the spectral document containing the required spectrum. 3. Proceed with one of the following: If you want to find the whole spectrum, make sure that the whole spectrum is displayed and click Search the Zoom tools ( on the Window Switching bar; or ), and then click Search . Or if you want to find spectra with signals in a specific area, select this area using any of 4. Depending on the type of search you want to perform (peak, mixture, multiplet, or similarity), in the Spectrum Search Options dialog box, click the required tab, and then set the search parameters to the appropriate values. 5. Click OK to switch to the Database window and start the search process.
Apply Direct Assignment

You can transfer the assignment performed in the current 1D spectrum to any two-dimensional experimental spectrum. To direct the assignment: 1. Load the 2D NMR spectrum(a) you want to be assigned and make sure that peak peaking is performed. 2. Click the reference 1D NMR spectrum (make sure that it is in the Assignment mode), and then, while holding down SHIFT, click the target 2D NMR spectrum. 3. From the Windows menu, choose Synchronize. 4. On the Analysis menu, point to Assignment, and then click Direct or, on the Assignment toolbar, click Direct Assignment to 2D . 5. In the Direct Assignments Options dialog box that appears, specify the appropriate settings for the assignment's transfer, and then click OK. 6. Switch to the target spectrum to view the directed assignments. If there is no attached structure in the target spectrum, the structure from the reference 1D NMR spectrum will be attached to it after the Direct Assignments application. If the assignment of the spectrum is not fixed according to one of the dimensions, the questionmark will appear in the peak label and in the Table of Assignments.
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Appendix. How To
Update Structure with Assignment

To update spectrum containing the assigned structure with a new structure without the loss of assignment (mainly), perform the following steps: 1. Switch to the ChemSketch window using one of the following ways: to draw a new On the Window Switching bar, click ChemSketch structure; or From the Edit menu, choose Chemical Structure to copy the current structure to the ChemSketch window for editing. 2. Draw the structure or find one in the dictionary (on the References toolbar, click ACD/Dictionary then click Processor ); or make the required changes to the structure. . 3. If there are two or more structures in the workspace, select the one you want to update, and 4. In the Select Action dialog box that appears, select the Update Structure for the Current Spectrum option, and click OK. 5. In the Structure Exchange Tool dialog box that appears, you can compare the discrepancy between the structure previously assigned to the spectrum and the updated structure. (For more information on this dialog box options, refer to the ACD/1D NMR Reference Manual (NMRMOD_R.PDF) located in the ACD/Labs documentation folder (\\DOCS). 6. To update the current spectral document with a new assigned structure and switch to the Processor window, click OK.
Link Documents
ACD/SpecManager allows you to link documents by attaching child-documents to the peaks of the currently active spectrum and update ACD/SpecDB databases with these documents. Tip The multi-documents containing series, Chrom-Mass data, etc. cannot be linked. If a document has already a child document, it cannot be linked as a child itself. To link such a document, first, you should remove all the links from it, then link this document as a child one, and after that restore the deleted links. Thus, you can create a hierarchy of linked spectral documents from the parent document to the child ones and not vice versa. Spectral and chromatographic documents from a protected database (e.g., those that are supplied with ACD/SpecManager) cannot be linked. 1. In the Processor window, open the spectral documents you want to be linked. The spectrum whose peaks will have child documents linked should be active. 2. From the View menu, choose Linked Documents to display the corresponding panel. 3. Right-click within the Linked Documents panel and, from the shortcut menu that appears, choose Linked Documents Organizer. 4. In the Peaks box of the Linked Documents Organizer dialog box that appears, select a peak to which a document is to be linked.
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5. In the Unlinked Documents box, choose the required document, and then click Add You can see that the selected file is moved to the Linked Documents box and the child document's name appears under the selected peak in the Peaks box. drag any unlinked file to the appropriate peak in the list.
Tip Alternatively, you can use the drag-and-drop functionality, i.e., to attach a document,
Also it is possible to link several spectral documents to a peak. To select several file names simultaneously, click the required names while holding down SHIFT or CTRL. 6. Repeat steps 4 and 5 until all of the desired documents are linked to the peaks of the parent spectrum, and then click OK in the Linked Documents Organizer dialog box. On the Linked Documents panel, you will see the list of the specified child documents. Note that the information on the links cannot be saved to a file within ACD/SpecManager but you can update a user database open in ACD/SpecDB with the current spectrum. 7. On the General toolbar, click Update Database record with the hierarchically linked documents.
Note
. The current spectrum will be saved as a
Each record can contain only one spectral or chromatographic document that in its turn can have a multi-level hierarchy of linked documents. For more information on linked documents, refer to the ACD/1D NMR Processor & Manager Reference Manual (NMRMOD_R.PDF) located in the ACD/Labs documentation folder (\\DOCS).
Customize Panels Display in the Processor Window

By default, the Parameters, User Notes, User Data, Structure User Data, 3D View, Linked Documents, and Zoom Area data panels can be moved over the screen. You can also fix these panels in the following positions: To the full height of the workspace to the left or to the right. To do this, drag the panel to the left- or rightmost border of the workspace until a frame denoting the required panel position appears, and then release the mouse button. To the full width of the workspace between the spectrum window and status bar or macro toolbar. To do this, drag the panel to the lower/upper border of the workspace until a frame denoting the required panel position appears, and then release the mouse button. To make the panel floating, drag it from its fixed location by the tab. To perform an analysis of the data from the Parameters, User Notes, User Data, Structure User Data, 3DView, and Zoom Area panels more comfortably, you can vary the representation and location of each panel: By following either of the above steps, you can fix the position of all the panels simultaneously. Double-clicking the tab of any panel allows you to switch between the tile and full view of the panels. The panels can be fixed in the same location and in different frames placed one after or under the other. The panels can be fixed in different locations simultaneously: to the right, to the left, and/or in the upper or lower part of the workspace. Finally, you can fix the position of some panels while the rest will be floating.
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Manipulate Tables
You can do the following actions with most tables in SpecManager. Edit table contents: right-click within the table to display the shortcut menu with options for editing. Depending on the type of the table, the shortcut menu contains different options. Change the size of a table: point to one of the borders or corners of the table, and then drag inward or outward to a new size. Move a table: drag the table header. Change the size of columns in a table: point to the border of the column heading and, when the mouse pointer turns into two-way arrow, drag left or right. Change order of columns: drag the required column heading to a new position. Sort data in columns: click the heading of any column to sort the table contents in the ascending (alphabetical) or descending (reversed alphabetical) order of the column values. Select data to be displayed: from the table shortcut menu (available at right-click in the table), choose Options and, in the Table Options dialog box that appears, specify the parameters to be displayed in the table, the alignment of text, and width of each column. Copy the contents of a table to Clipboard: select the corresponding command from the shortcut menu that is available at right-click in the table. Place a table on the report page together with the spectrum: select the corresponding check box in the Report Page Setup dialog box. Export a table contents to a text file: right-click in the table, and then, from the shortcut menu, choose Export Table. Close a table: right-click in the table, and then, from the shortcut menu, choose Close Table. Clear a table: right-click in the table, and then, from the shortcut menu, choose Clear Table.
Note
To change the size of a table, close or move it, you can also right-click the table header, and then select the required option.
If a column in the table does not contain any data for all the rows, this column is not displayed. To hide all of the opened tables at once, on the View menu, point to Tables, and then choose Hide All.
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ACD/1D NMR Processor & Manager

Version 12.0 for Microsoft Windows

Processing and Organizing Experimental 1D NMR Data

Mouse Conventions ...................................................................................................... vi

For More Information.................................................................................................vii

Program Basics ......................................................................................... 1

Loading and Displaying Spectrum........................................................... 5

3.3 3.4 3.5 3.6 3.7

Analyzing Spectrum ................................................................................ 21

4.2.1 4.2.2 4.2.3 4.2.4

ACD/1D NMR Processor & Manager

Deleting Peak Labels ............................................................................................... 26

4.3 4.4 4.5 4.6

Measuring Distance ........................................................................................... 26 Adjusting Spectrum to Reference Point ............................................................. 26

Annotating .......................................................................................................... 28 Integrating Peaks ............................................................................................... 31

Peak Fitting ........................................................................................................ 37

Attaching Chemical Structure............................................................................. 44

Assigning Peaks and Verifying the Structure.................................................. 60

ACD/1D NMR Processor & Manager

5.2 5.3 5.4 5.5

Creating Report ....................................................................................... 97

7.4.1 7.4.2 7.4.3

Creating a Poster ............................................................................................. 104 Creating a Template-Based Report ................................................................. 105

Macro Processing.................................................................................. 107

8.3.1 8.3.2 8.3.3 8.3.4 8.3.5 8.3.6

Editing a Macro ................................................................................................ 112 Managing Macros............................................................................................. 113

8.5.1 8.5.2 8.5.3 8.5.4

Processing a Group of Spectra (Group Macro)................................................ 114

ACD/1D NMR Processor & Manager

Executing Group Macro.......................................................................................... 120

Applying Intelligent Bucketing to Thousands of Spectra .................................. 122

Integrating Experiment and Prediction................................................ 124

Appendix. How To...................................................................................... 129

ACD/1D NMR Processor & Manager

Before You Begin

About This Tutorial

ACD/1D NMR Processor & Manager

Before You Begin

ACD/1D NMR Processor & Manager

Before You Begin

For More Information

ACD/1D NMR Processor & Manager

1.2 Starting ACD/1D NMR Manager

1.3 Setting File Associations

ACD/1D NMR Processor & Manager

1.3.1 Changing File Associations

1.4 Manager or Processor

ACD/1D NMR Processor & Manager

1.5 Changing Default Directories

ACD/1D NMR Processor & Manager

1.6 Quitting ACD/1D NMR Manager

ACD/1D NMR Processor & Manager

2. Loading and Displaying Spectrum

2.2 Loading Raw Data

ACD/1D NMR Processor & Manager

Loading and Displaying Spectrum

2.3 Elements of the Processor Window

Spectrum Display area

Scales Status bar Window Switching bar

ACD/1D NMR Processor & Manager

Loading and Displaying Spectrum

2.4 Changing Display Preferences