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ACD/1D NMR Processor

& ManagerVersion 12.0 for Microsoft WindowsTutorial

Processing and Organizing

Experimental 1D NMR Data


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Advanced Chemistry Development, Inc.

Copyright19942010 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 Statesand/or other countries Copyright 2010 Microsoft Corporation. All rights reserved.

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All the other trademarks mentioned within this reference manual are the property of theirrespective owners.

All trademarks are acknowledged.

Information in this document is subject to change without notice and is provided as is with nowarranty. Advanced Chemistry Development, Inc., makes no warranty of any kind with regard tothis 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 errorscontained herein or for any direct, indirect, special, incidental, or consequential damages inconnection with the use of this material.


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Table of Contents

Before You Begin ............................................................................................... vAbout This Tutorial......................................................................................................... v

Advanced Understanding ......................................................................................................... vMouse Conventions ...................................................................................................... viOperations ................................................................................................................................viFor More Information.................................................................................................vii

How to Contact Us...................................................................................................................viiOnline Updates ........................................................................................................................vii

1. Program Basics ......................................................................................... 11.1 Objectives ............................................................................................................11.2 Starting ACD/1D NMR Manager ..........................................................................11.3 Setting File Associations...................................................................................... 1

1.3.1 Changing File Associations........................................................................................ 21.4 Manager or Processor..........................................................................................21.5

Changing Default Directories ...............................................................................3

1.6 Quitting ACD/1D NMR Manager ..........................................................................4

2. Loading and Displaying Spectrum........................................................... 52.1 Objectives ............................................................................................................52.2 Loading Raw Data................................................................................................52.3 Elements of the Processor Window .....................................................................62.4 Changing Display Preferences.............................................................................72.5 Displaying Spectral Data......................................................................................7

3. Processing Spectrum................................................................................ 93.1 Objectives ............................................................................................................93.2

Applying Interactive Fourier Transform..............................................................10

3.2.1 Defining Zero Filling ................................................................................................. 113.2.2 Applying Linear Prediction........................................................................................ 113.2.3 Specifying Window Function....................................................................................123.2.4 Correcting Phase...................................................................................................... 12

3.2.4.1 Automatically..................................................................................................... 133.2.4.2 Manually ............................................................................................................ 13

3.3 Obtaining the Power Spectrum .......................................................................... 143.4 Obtaining the Magnitude Spectrum.................................................................... 143.5 Removing Solvent ..............................................................................................153.6 Dark Regions ..................................................................................................... 163.7 Correcting the Baseline......................................................................................17

3.7.1 Automated Baseline Correction ............................................................................... 183.7.2 Manual Baseline Correction..................................................................................... 19

4. Analyzing Spectrum ................................................................................ 214.1 Objectives ..........................................................................................................214.2 Labeling Peaks................................................................................................... 22

4.2.1 Automatic Peak Picking............................................................................................ 224.2.2 Manual Peak Picking................................................................................................ 234.2.3 Labeling an Arbitrary Position .................................................................................. 244.2.4 Changing the Appearance of Peak Labels............................................................... 25

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4.2.5 Deleting Peak Labels ...............................................................................................264.3 Measuring Distance ...........................................................................................264.4 Adjusting Spectrum to Reference Point ............................................................. 26

4.4.1 Automatic Detection ................................................................................................. 264.4.2 Manual Adjustment...................................................................................................27

4.5 Annotating..........................................................................................................284.5.1 Inserting an Annotation ............................................................................................ 284.5.2 Deleting an Annotation.............................................................................................31

4.6 Integrating Peaks ...............................................................................................314.6.1 Manual Integration....................................................................................................314.6.2 Modifying Integral Curves......................................................................................... 334.6.3 Integration Options................................................................................................... 344.6.4 Bucket Integration .................................................................................................... 354.6.5 Automatic Integration ............................................................................................... 364.6.6 Setting Reference Value .......................................................................................... 364.6.7 Changing Integral Appearance................................................................................. 37

4.7 Peak Fitting ........................................................................................................374.7.1 Specifying Peak Fitting Options ............................................................................... 384.7.2 Defining Region........................................................................................................ 394.7.3

Optimizing................................................................................................................. 40

4.7.4 Modifying Peak Parameters ..................................................................................... 41

4.7.4.1 Using the Mouse ............................................................................................... 424.7.4.2 Using the Dialog Box......................................................................................... 424.7.4.3 Batch Modification............................................................................................. 43

4.8 Attaching Chemical Structure............................................................................. 444.8.1 Displaying a Structure in the Processor Window ..................................................... 45

4.9 Defining Multiplets.............................................................................................. 464.9.1 Specifying Multiplets Analysis Options..................................................................... 464.9.2 AutomaticMultiplet Building ..................................................................................... 474.9.3 J-Coupler.................................................................................................................. 48

4.9.3.1 Basic Multiplet Recognition............................................................................... 484.9.3.2 Defining Multiplets Using J-Coupler.................................................................. 504.9.3.3

Setting Couplings Manually .............................................................................. 52

4.9.3.4 Adding Missing Peaks....................................................................................... 55

4.9.4 Connecting Multiplets Manually................................................................................ 584.9.5 Connecting Multiplets Automatically ........................................................................ 59

4.10 Assigning Peaks and Verifying the Structure..................................................604.10.1 Verification................................................................................................................ 60

4.10.1.1 Dealing with Verification Results....................................................................... 644.10.2 Manual Assignment.................................................................................................. 66

4.10.2.1 Assigning by Peak............................................................................................. 664.10.2.2 Assigning by Multiplets...................................................................................... 67

4.10.3 Automatic Assignment.............................................................................................. 694.10.4 Comparing Manual and Automatic Assignments ..................................................... 70

4.11 Shortcut Mode................................................................................................. 714.11.1 Specifying Shortcut Mode Options........................................................................... 724.11.2 Action Helper............................................................................................................ 734.11.3 Defining Dark Region ............................................................................................... 744.11.4 Setting Reference Point ........................................................................................... 754.11.5 Defining Multiplets.................................................................................................... 764.11.6 Assigning Multiplets.................................................................................................. 784.11.7 Quitting Shortcut Mode.............................................................................................79

5. Multispectral Operations......................................................................... 805.1 Objectives ..........................................................................................................80

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5.2 Loading Two Spectra .........................................................................................805.3 Synchronizing Spectra ....................................................................................... 815.4 Arithmetic: Adding and Subtracting Spectra ......................................................825.5 Working with Spectral Series .............................................................................83

5.5.1 What is a Series? .....................................................................................................835.5.2 Creating a Series......................................................................................................845.5.3 Creating a Series in Other Ways..............................................................................855.5.4 Coloring Spectra....................................................................................................... 86

5.5.4.1 Applying Auto Colors......................................................................................... 865.5.4.2 Applying System Color...................................................................................... 875.5.4.3 Applying Custom Colors.................................................................................... 88

5.5.5 Copying, Moving, and Deleting Spectra from a Series ............................................ 885.5.6 Processing Spectral Series ...................................................................................... 89

6. Quanalyst ................................................................................................. 926.1.1 Objectives.................................................................................................................926.1.2 Working with the Quanalyst dialog box .................................................................... 926.1.3 Adjusting the Quantitation Graph............................................................................. 94

7.

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

7.1 Objectives ..........................................................................................................977.2 Creating a Standard Report ...............................................................................977.3 Report Page Setup.............................................................................................997.4 Modifying the Spectrum Report........................................................................102

7.4.1 Changing the Spectrum Display.............................................................................1027.4.2 Changing the Table Display ...................................................................................1037.4.3 Changing the Structure Display..............................................................................103

7.5 Creating a Poster .............................................................................................1047.6 Creating a Template-Based Report .................................................................105

8. Macro Processing .................................................................................. 1078.1 Objectives ........................................................................................................1078.2 What Is a Macro and Group Macro? ................................................................1078.3 Creating a Macro..............................................................................................107

8.3.1 Macro Organizer.....................................................................................................1078.3.2 Creating from Template..........................................................................................1088.3.3 Creating Manually .................................................................................................. 1088.3.4 Creating from History .............................................................................................1108.3.5 Creating via Quanalyst ........................................................................................... 1118.3.6 Settings for Macro Execution ................................................................................. 111

8.4 Editing a Macro ................................................................................................1128.5 Managing Macros.............................................................................................113

8.5.1 Placing Macros as Buttons on the Toolbar ............................................................ 1138.5.2 Setting a Shortcut Key for Macro Execution ..........................................................1138.5.3 Autorunning a Macro upon Spectrum Loading....................................................... 1148.5.4 Logging Macro Processing Results into a File .......................................................114

8.6 Processing a Group of Spectra (Group Macro)................................................1148.6.1 Specifying Plate Type.............................................................................................1148.6.2 Specifying a Group of Spectra ............................................................................... 1158.6.3 Specifying Processing Options .............................................................................. 1178.6.4 Attaching Structures to Spectra ............................................................................. 117

8.6.4.1 One by One.....................................................................................................1178.6.4.2 Group of MDL Molfiles ....................................................................................1188.6.4.3 Group from an SDfile ...................................................................................... 118

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8.6.5 Executing Group Macro.......................................................................................... 1208.7 Applying Intelligent Bucketing to Thousands of Spectra..................................122

9. Integrating Experiment and Prediction ................................................ 1249.1 Objectives ........................................................................................................1249.2 Preparing an Experimental Spectrum ..............................................................1249.3 Preparing Predictor Database..........................................................................1259.4 Transferring Chemical Shifts............................................................................1269.5 Using a Database to Calculate a Spectrum .....................................................128

Appendix. How To...................................................................................... 129Objectives .................................................................................................................. 129Register User Formats............................................................................................... 129Import from an ASCII File ..........................................................................................131Shift FID Spectra........................................................................................................131

Apply Interactive Apodization.....................................................................................132Manipulate Windows.................................................................................................. 133Enlarge Spectrum View .............................................................................................134Lock a Display Range................................................................................................135Save Spectral Region as an Individual Spectrum......................................................135Edit a Spectrum .........................................................................................................135Update Spectrum User Data via Data Form ..............................................................136Update Structure User Data via Data Form ...............................................................136Select a View Mode for Selected Spectra..................................................................137Search in Databases. General Notes ....................................................................... 137Search Shifts in NMR Predictor Databases ...............................................................138Perform Peak, Mixture, Multiplet, and Similarity Searches .......................................139

Apply Direct Assignment............................................................................................139Update Structure with Assignment.............................................................................140Link Documents .........................................................................................................140Customize Panels Display in the Processor Window ................................................141Manipulate Tables...................................................................................................... 142

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Before You Begin

Mouse Conventions

You may perform several actions during your work with this software; the following specific wordsare used to describe them:

Point tomeans move the mouse pointer to an item. Clickor left-click means point to an item, and quickly press and release the left mouse

button.

Right-clickmeans point to an item, and quickly press and release the right mouse button.

Double-clickmeans point to an item, and quickly press and release the left mouse buttontwice.

Dragmeans point to an item, and press and hold down the left mouse button while youmove the item.

Select means highlight or make an interface element active by either clicking it or draggingover it (other actions are possible if specified in documentation). If used in "select thecheck 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 Processorwindow can be performed by using various Operation Modes (e.g., Integration and PeakPicking) that can be accessed from the Operation toolbar. Note that when you enter any of thesemodes, 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 and

Cancel Changes .

To keep all of the changes made in the current mode and quit the mode, clickAccept Changes

.

To annul all of the changes made while working in the current mode and quit the mode, click

Cancel Changes .

Important If you choose any command belonging to another mode, the current mode willbe exited automatically and all of the changes will be saved as if you have

clickedAccept 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 areason for this: much is offered through our Web site. We offer free ChemSketch, an ACD/LogPFreeware Add-on for ChemSketch, a free ISIS 3D Add-in, free ChemDraw extensions, and a free2-week demo key for Interactive Laboratory sessions where you can run test calculations usingJava applets without purchasing software. There are TechSmith Camtasia-based moviesavailable for download which show the operation of many of our software packages (especiallyChemSketch).

We are constantly updating the information on our Web site. The Web site will tell you at whichscientific conferences you can visit the ACD/Labs booth. You can browse the Frequently AskedQuestions page or drop in and chat on our newsgroup, which can also be reached via our Website.

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 popularway to contact us is via electronic mail. Questions on pricing, sales, availability, and generalissues should be directed to:

[email protected]

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, chooseAbout to find this information); as well as a description of the problem you are having. Ifapplicable, 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. Theseintermediate releases (bringing the actual version number of a program, for example, from N.00to N.01) often contain new functionality along with additional bug fixes and support for new fileformats. To check if there is a new update available and to have this sent to you, please contactyour local agent or our Technical Support Department. Before calling, we recommend that youhave ready the name of the software purchaser, the product name, version number, buildnumber, and license ID of the product you are contacting us about. All Desktop ACD/Labssoftware 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 onwhich the software is installed. For more information, refer to theACD/Updater Users Guidelocated in the ACD/Labs documentation folder, \\DOCS\UP_CLNT.PDF.

ACD/1D NMR Processor & Manager Tutorial vii
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1. Program Basics

1.1 ObjectivesThis 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 providedin the Quick Start Guide booklet which is included in every shipment of ACD/Labs software.

1.2 Start ing ACD/1D NMR Manager

Once ACD/SpecManager, ACD/NMR Processor, or ACD/1D NMR Manager has been installed onyour computer, follow these basic steps to start it:

1. Start Microsoft Windows.

2. On the Windows desktop, double-click ACD/SpecManager icon.OROn the Start/Run menu in the Windows taskbar, point toACD/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.ORIf you have other ACD/Labs programs running, from theACD/Labs menu, chooseSpecManager.

3. As a result, you should see the splash screen, and then the empty Processor window isactivated. 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 Associationsdialog box appears.

This contains a selectable list of file extensions and file types, which you may set to openautomatically 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 arenot sure, leave the check boxes blank and click No.

Note If you displayed the File Associationsdialog box (from the Filemenu, choose FileAssociations) under Windows NT but have no rights to change file associations, awarning message appears. Contact your system administrator to resolve thismatter.

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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 anytimefrom the Filemenu, choose File Associations. If all ACD/Labs supported file extensionshave already been associated, then you will receive a message, all supported file types arealready associated with the current application. In this case, you can change the fileassociations 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 theAlways use thisprogramcheck box.

5. Click OKand close Windows Explorer.

1.4 Manager or Processor

To check what module1D NMR Manager or 1D NMR Processor (without the SpecDB module

and Databasemenu commands)you have installed and/or to specify the module you want towork with, you can use the Select Moduledialog box.

1. When no files are open in the Processor window, from the Optionsmenu, choose Modules .

2. In the dialog box that appears, from the Typelist, select 1D NMR:

3. Choose what module you are going to use by selecting either theACD/1D NMR ProcessororACD/1D NMR Manageroptions. To be able to complete exercises provided by this tutorial,selectACD/1D NMR Manager.

Note If you have only 1D NMR Processor installed, this dialog box just informs you ofthat and you cannot use 1D NMR Manager.

4. Select the Use as Defaultcheck box to automatically enable the corresponding module as

you start ACD/SpecManager.

5. Click OKto save changes.



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1.5 Changing Default Directories

If you are running a single-user (stand-alone) copy of ACD/1D NMR Manager, the defaultdirectory settings are likely fine.

If you have a network copy of ACD/1D NMR Manager, it is advisable to change the defaultdirectory 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 orunlimited numbers of seats, follow the below steps at each local installation:

1. From the Optionsmenu, choose Default Directories.

2. In the Default Directoriesdialog box that appears, make sure that 1D NMRtab is active.

3. In the corresponding boxes, specify the directories that will be opened by default whileopening, saving, importing, or exporting files as well as opening or saving macros in theProcessor window:

4. Click OK.

5. On the Window Switching bar, click ChemSketch to switch to the

ChemSketch window.

6. From the Optionsmenu, choose Preferences, and then, on the Generaltab of the dialog boxthat appears, specify the default directory for opening, saving, importing, and exporting files inthe ChemSketch window:

Note In the Privatebox, you can set the directory for recording the configuration of the

ChemSketch program (for example, TEMPLATE.CFG and GRSTYLES.STL files).7. Click OKto close the dialog box, and then switch back to the Processor window by clicking

Processor .



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1.6 Quit ting ACD/1D NMR Manager

Information provided in this section is intended to familiarize you with possible ways of quittingACD/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 theACD/Labs menu, choose Exit All. This will attempt to quit all of the ACD/Labsprograms that are currently running, one after another.

3. From the Filemenu, choose Exit. This will close only the ACD/Labs program you are workingwith at the moment.

You will be prompted to save your work.



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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 Filemenu, point to Import, and then choose From 1D NMR Directoryor click

Open/Import Spectrum to display the Importdialog box.

2. Select a file format of (Auto Detect) and click drives and directories until you are in theEXAMPLES folder provided with your software which contains the file FID in the\CATECHIN.FID directory. (The path name is likelyC:\ACD12\EXAMPLES\SPECMAN\1DNMR but if you are having trouble finding it, use yoursystem finder.)

3. Click Openand the file will be loaded.



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Loading and Displaying Spectrum

2.3 Elements of the Processor Window

When describing the program throughout this tutorial, some terms defining various parts of itsinterface are used. Below you will find the picture showing the interface arrangement:

Status bar

Scales

Spectrum Display area

Title bar

Menu bar

General too lbar

Macro too lbar

Window Switching bar

Operation toolbar

Note that the file name, the spectrum type, and the nucleus type are reflected in the status linealong the bottom of the Processor window.



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2.4 Changing Display Preferences

The multi-tab Preferencesdialog box allows you to specify the way all of the spectra loaded intothe Processor window should be displayed.

1. From the Options menu, choose Preferences.

2. Practice changing the display by varying the set of options and clickingApply .

3. To have absolute correspondence with the images of the tutorial, specify the settings asdisplayed in the screen shot below. Otherwise, you may preserve the options that are to yourtaste.

4. Click OKto close the dialog box.

Other tabs of the Preferencesdialog 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 requiredinformation on the document you are working with. On the left-hand side of the status bar, youcan 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 AbsoluteIntensity view modes (for series):



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The central part of the status bar (that is currently empty) can display different data depending onthe option chosen in the Status Bar Settingsdialog box:

1. From the Optionsmenu, choose Status Barto display the Status Bar Settingsdialog box.

2. Make sure that the Spectrum Parametersoption is selected and, in the adjacent box, fromthe drop-down list, choose Comment:

3. Click OKto place the data from the Commentline in the Parameters panel (if it is presentthere for the spectrum displayed) on the status bar:

4. To verify the spectrum origin and details, from the Viewmenu, choose SpectrumParameters . You will see the Parameterspanel displayed.

Note The spectrum Parameters cannot be modified within ACD/SpecManager. GoodLaboratory Practice (GLP) requirements stipulate that parameters that are input atthe time of recording the original data should not be changed by software whichprocesses 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 creationcorrectly only if the AUDITA.TXT file is located in the same folder as FID.



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3. Processing Spectrum

3.1 Objectives

This section of the tutorial provides you with the basics of spectrum processing. From a variety ofhandy features available in ACD/1D NMR Manager, we will examine the most up-to-date andeasy-to use ones. You will learn how to:

Use Interactive FT mode for:

o Transforming FID into FT spectrum;

o Defining Zero Filling parameter;

o Applying linear prediction

o Specifying weighting function;

o 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.exewhich canbe downloaded from our Web site. Also, by default, it is placed in the MOVIES folder at the timeof installing ACD/1D NMR Manager.



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3.2 Applying Interactive Fourier Transform

The program allows you to interactively and quickly adjust the most suitable parameters for theFourier transformation and spectrum phasing.

1. On the Operation toolbar, click Interactive Fourier Transform . The

integrated Fourier Transformdialog box appears in the compact form:

Important This dialog box allows you to reprocess FT-ed spectra without loosing anyspecified data (peak labels, assignment, etc.) at any stage of analysis.

Note that the default settings are specified and theApply FTand Instant Previewcheck boxesare selected.

2. Click Preview to apply Fourier transform using the default settings and display

the result without closing the dialog box:

Tip To convert the FT spectrum back to the corresponding FID, just clear theApply FTcheck box.



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3. If the obtained spectrum suits your requirements, click OKin the Fourier Transformdialogbox and proceed with Section 3.3.

In our example, to demonstrate all the power of Interactive FT and familiarize you with theoptions available in the dialog box, we will slightly modify the obtained spectrum.

3.2.1 Defin ing Zero FillingTo enhance spectrum resolution, let us specify Zero Filling settings first.

1. Keep the value of the Initialbox (number of data points recorded during the signal detectionperiod) unchanged.

2. In the Finalbox, insert 32768by clicking arrows on the right to set the number of points thatwill 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 toAppendix. HowTo

3.2.2 Applying Linear Prediction

Linear prediction allows you to remove artifacts or distortion, caused by delayed acquisition orproblems with the initial points of a FID and improve resolution in 1D NMR spectra with a shorttime domain.

Backwardis used to correct the first few corrupted data points in the FID. Note that the defaultvalue 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 commonquantity base points.

Forwardis used to improve resolution in cases where the FID is badly truncated. This isusually not the case for routine 1D NMR spectra, so forward linear prediction is not generallyrecommended. Note that the number of LP coefficients used for forward prediction should beslightly greater than the number of expected peaks in a spectrum.

1. In the Fourier Transformdialog box, click Linear Prediction .

2. In the area with options for linear prediction that appears, select the Backwardcheck box andspecify 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 wehave 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 LinearPrediction(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 for13

C spectra). Aweight functionalso called a window functionis normally used to reduce noise in thespectrum.

1. Click Window Function to display the area where you can choose the

type of apodization to be applied.

2. For the given example, we recommend that you select the Usertype of apodization, and thenchoose EM(exponential multiplicationfunction).

3. In the corresponding line-broadening box (LB column), specify the value 0.2.

Note 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.

3.2.4 Correcting Phase

Now we can correct the phase of the obtained FT spectrum. The phase can be corrected in twoways: 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 thebaseline, or correction by symmetrizing the spectrum lines. The second method is highly efficientfor

1H-spectra. The third one is more useful for

13C-spectra.

1. In the Fourier Transformdialog box, clickAuto Simple . You should see the

spectrum changes a little.

Tip To keep the value of the first order phase parameter (Ph1) untouched during the AutoPhasing Simple or Auto Phasing by Baseline Optimization procedures, click Phasing

Parameters , and in the area that appears, select the Fix check

box.

2. Try other methods of phase correction by clickingAuto BL Opt or

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 involvethe use of both the left and right mouse buttons. These are shortcuts to the phase buttons in thePhasing Parametersarea:

1. In the Fourier Transform dialog box, click MousePhasing . You will see the

colored vertical line that defines the phase pivot point, which automatically is set to the highestpeak 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 lineremains, drag with the rightmouse button. You can drag the red line to place it over anotherpeak.

Tip You can also specify both parameters either by entering the values manually or byclicking the arrows to the right of the corresponding field in the Phasing Parametersarea.

4. If you are not satisfied with the obtained result, in the Fourier Transformdialog 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 OKto quit the Interactive FT mode andclose the Fourier Transformdialog box.

Note If you are not satisfied with the results of spectrum processing, try other settingsuntil 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 Processmenu, choose PowerSpectrum. Since this operation has the effect of squaring each y-value, the relative intensityof 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 Processmenu, and then Power Spectrumagain.

3.4 Obtaining the Magnitude Spectrum

1. To convert a transformed spectrum with real and imaginary output to a magnitude spectrum,from the Processmenu, choose Magnitude Spectrum. Zoom in the spectrum part using the

Rectangular Zoomtool ( ).

2. Similar to the Power Spectrum mode, the Magnitude Spectrum mode disables some of theprocessing options.

3. Zoom out the spectrum (click Show Whole Spectrum ) and go back to the usual

spectrum view by choosing Magnitude Spectrumfrom the Processmenu again.



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3.5 Removing Solvent

This option allows you to remove unnecessary spectrum signalse.g., solvent signals.

1. From the Processmenu, choose Remove Solvent Signalto 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 theSpectrum Parametersof the current spectrum, the solvent signal is automatically defined. Ifthe program cannot find the solvent, the region in the center of the spectral curve is selected.

2. Click Remove Solvent Options to display the Remove Solvent Options dialog

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 linedefines the center of the solvent signal and two other linesits width. Or you may also usethe 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 anadmixture, so the recommended values for the region to be removed in the current example

are Solvent Position = 3.38 ppm and Frequency Domain FilterZone Width = 70 Hz.

Note You can also use the Remove Solvent Optionsdialog box (see point 2) to specifythe 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 .



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After some processing time, you will see the spectrum change considerablythe solvent signalhas been removed and the curve is modified accordingly:

Note 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 .

3.6 Dark Regions

In Section 3.5, we have learned to remove unnecessary spectrum signals by using the RemoveSolvent Signalcommand. Now, let us try to get the same result by setting the dark region.

1. From theAnalysismenu, choose Dark Regions.

2. In the Dark Region Organizerdialog box that appears, click Edit to display the

Edit Dark Region dialog box. For more information on the dialog box, refer to theACD/1DNMR Processor and Manager Reference Manual(NMRMOD_R.PDF) located in the

ACD/Labs documentation folder (\\DOCS).

3. In the Descriptionfield, type HDOto define the annotation.

4. In the From (ppm) and To (ppm) boxes enter 3.3and 3.4485correspondingly, as shown inthe picture below.

5. Select theActive check box (otherwise, the dark region will be added to the Dark RegionOrganizerdialog box but will not appear on the spectrum); theApply to the CalculatedSpectrum check box should remain clear.



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6. Click OKto return to the Dark Region Organizerdialog box. Note that the dark region isadded to the list of dark regions.

7. Click OK to close the Dark Region Organizer dialog box. Note that the dark region is nowdefined on the spectrum.

Dark Region

Note To change the color of the dark region, from the Optionsmenu, choosePreferences. On the Spectrum tab that is displayed, click the Dark Region colorbox to display the color palette, and then select the appropriate color.

All information on dark regions is stored in the Dark Region Organizerdialog box.

Using the buttons to the right of the list in the Dark Region Organizerdialog box, you can add,edit, delete dark regions, and also search for a solvent you want to appear as a dark region (theSolventsbutton). The Solvent Shiftsdialog box contains solvents referring to an activespectrum nucleus alongside their chemical shifts making the definition of the applied solvent fastand 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 adjustingsome 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 Optionsdialog

box. In this section, we place emphasis on the lower part of the dialog box containing settingsfor automatic correction:

2. For the current example, we recommend that you choose the Spectrum Averagingmethodand set the Box Half Widthparameter to 15and Noise Factorto 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 Basel ine . The red line fits the spectrum baseline:



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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 thatthe 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 and drag a rectangular

selector over the node(s) you want to remove.

5. To view the spectrum with the resultant baseline, click ShowResult .

6. Zoom out to display the whole spectrum ( ). ClickAccept Changes to save the

current baseline and quit this mode.

7. Save the processed spectrum into a separate file. From the File menu, choose Save Asandspecify 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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4.1 Objectives

A spectroscopist needs to communicate the information deduced from a spectrum to the nextperson who views the spectrum. One of the most efficient means to do this is by directlydesignating 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 thestructure.

This chapter covers material that appears, in part, in the movie 1dnmr_2.exewhich canbe downloaded from our Web site. Also, by default it is placed in the MOVIES folder at the timeof 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, loadCATEC_FT.ESP, and proceed with the following steps.

You can also use the CATECHIN.ESP file from the EXAMPLES folder. To follow the exercisesdescribed below, on the Editmenu, point to Clear, and then chooseAl l Tables to clear all of thelabels in the CATECHIN.ESP file.

Note Depending on the spectral file you will use to perform the following exercises, datashown in various tables and pictures throughout this chapter of the tutorial mayslightly 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, manualpeak 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 .

2. On the General toolbar, click Horizontal Zoom and select the area of the spectrum

containing all of the signals (from about 1.5 to 9.5 ppm) by dragging.

3. On the Operation toolbar, click Peak Picking . Note that a new Peak Picking

toolbar appears.

4.2.1 Automatic Peak Picking

1. On the Peak Picking toolbar, clickAuto Peak Pick ing . Labels will be placed on all of

the peaks in accordance with the default parameters (noise factor, minimum height) set in the

Peak Picking Optionsdialog box.2. To change the default parameters, on the Peak Picking toolbar, click Peak Picking

Options to display the Peak Picking Optionsdialog box.

3. Specify the required Noise Factorand Minimum Height (peaks smaller than the specifiedheight barrier are not labeled) or Minimum S/N(peaks whose height to RMS Noise ratio issmaller than the specified value are not labeled) either by clicking the arrows to the right of thecorresponding 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

accordance with the previous parameters, and then clickAuto Peak Picking on the

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 to remove

the labels set in the previous section.

1. On the Peak Picking toolbar, choose Select Peak Picking Level and move the

mouse over the workspace. Note that the horizontal red line appears in the Processor windowand is attached to the mouse pointer.

2. Move the mouse to specify the minimum peak height and click to fix it. Note that the labelsappear on all of the peaks higher than the selected level with no regard for the defaultminimum peak height.

3. On the Peak Picking toolbar, clickAdjust Peak . Now you can remove or

insert a label for the selected peak.



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4. To insert a label, move the mouse pointer to any unlabeled peak and click when it ishighlighted. Note that the label appears.

5. To remove a label, move the mouse pointer to any labeled peak and click when it ishighlighted.

4.2.3 Labeling an Arbitrary Position

If you want to mark a chemical shift between doublets or quartets, on the shoulder of a largerpeak, or at any position where the point of a peak does not occur, this command is especiallyhelpful.

1. In the Manual Peak Picking mode with theAdjust Peakbutton pressed in ( ),

while holding down SHIFT, click where you want to locate the peak. A label will appear. Forexample, 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 themouse 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. ClickAccept Changes to save the labels and quit the Peak Picking mode.

Note All of the described commands are applied to the selected fragment of thespectrum only.

4.2.4 Changing the Appearance of Peak Labels

1. From the Optionsmenu, choose Preferences, and then switch to the Labelstab:

2. If necessary, change the color, size, and font used for labels. Note that these settings will alsobe applied to other labels: annotations, assignments, and multiplets (see the chapters later inthis guide).

3. Now switch to the Peakstab:

4. If required, change positions and orientation of the labels, as well as the decimal accuracy ofvalues. 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. Thepeak 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 .

1. Click Show Whole Spectrum to zoom out.

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 toset 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 regardlessof 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 to display a new Reference

toolbar.

4.4.1 Automatic Detection

For 13C and 1H spectra ACD/SpecManager includes the automatic reference peak detectionfeature.

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 automaticallydisplayed in the Solvent box. In this case it is DMSO-d6. If necessary, you may set anothersolvent, though, for our example, it is recommended to set options as displayed in the abovepicture and click OK.

Note If the spectrum contains both TMS and solvent signals, the TMS peak is only usedfor scale adjustment.

3. On the Reference toolbar, clickAuto Reference . Based on the data in the

Parameterspanel of the current spectrum, this feature automatically determines the possiblereference peak, adjusts the spectrum according to it, and annotates the peak (notice theDMSO-d6annotation 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 thereference peak manually.

1. Click Clear Changes to cancel changes made by theAuto Referencefeature.

2. Move the mouse pointer to the peak to be referenced, in this case, DMSO-d6, and click whenit 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 Shiftsdialog box, select DMSO-d62.50from the list. As you can see, thisdialog box contains a list of standard reference points for the active spectrum nucleus withannotations. If you want the annotation to be attached to the peak, select theAdd

Annotationcheck box.

Tip You may also add new entries or edit the list of standard reference points using thegroup of boxes and buttons at the bottom of the dialog box. To restore the defaulttable, click Restore.

4. Click OK. Note that all of the shifts are recalculated relative to the specified reference point.

5. ClickAccept Changes to save the changes and quit this mode.

Note To delete a Reference peak designation, you should delete both the peak from the

Table of Peaks and the annotation (if you have selected the latter) from the

Table of Annotations .

4.5 Annotating

In the Annotation mode, you can annotate either a single peak or a spectral region and assignannotations to ten different layers.

4.5.1 Inserting an AnnotationWe will demonstrate the region annotation:

1. On the Operation toolbar, clickAnnotate Peak/Region .



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2. On the Annotation toolbar, click Options to display the Layer Label Options

dialog box.

3. In this dialog box, specify the required options for the labels of different annotation layers andinformation that is to be inserted into them. For the current example, select the second layerand set options as displayed in the picture below:

Note According to the specified settings, all the annotation labels of the second layer willinclude the date of creation, layer number, and fields for displaying the updatingdate 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.



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5. As you release the mouse button, the Edit Annotationdialog box appears where you canenter the desired annotation and specify a layer for it.

Note To add the annotation as a dark region, select theAdd as Dark Region check box.For more information, refer to Section 3.6.

6. Click OKto attach the annotation to the specified region (make sure that the button

corresponding to the current layer is active on the Annotation toolbar( )):

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 (button corresponding

to the layer number) to cancel its selection:

8. ClickAccept Changes to save the changes and quit this mode. To display the whole

spectrum, on the General toolbar, click Show Whole Spectrum .

Note If you then decide to edit the annotation, click it with theAnnotat ionmode activeand 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.ORRight-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 bymanual integration of the selected spectrum segments. We will demonstrate both ways.

On the Operation toolbar, click Integration . Note that a new Integration toolbar

appears.

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 and select the

area of the spectrum you want to integrate by dragging over it.



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3. You can also integrate the entire curve first and then divide the integral curve into smallerparts. 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 asyou need until all the necessary portions are integrated.

5. Click Select Segments for Integration to exit the Manual Integration mode.

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 on

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 andvertical 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 arrowsappear instead of the cursor and drag it vertically. Note that all of the other integrals areresized with the selected one. The blown-up portion of the peak around 3.8 ppm will lookapproximately 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 anddrag it vertically. Note that you can only move the selected integral curve. You can moveevery integral curve in a similar manner:

Note To move all or several integral curves at a time, select them either by dragging aselection box around them or by clicking them while holding down SHIFT, and thenmove the rectangular selection.



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4. Place the mouse pointer over the left/right side of the rectangular selection that surrounds theintegral curve so that the arrows appear instead of the cursor and drag it horizontally toexpand 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.

1. On the Integration toolbar, click Integral Options to display the Integration

Optionsdialog box. You can choose among two types of automated integration:

2. If you set the option as displayed above (with the Detect Signal Intervalscheck box selected)the segments of the spectrum that contain signals will be integrated only. The integrals in thiscase will be plotted as separate segments. If this check box is cleared, the solid integral curvewill be plotted for the whole spectrum. The Noise Factoris the parameter (%) that definesthe spectrum signal. If the resultant integral has a value smaller than 1/1000th of themaximum integral, it is deleted. The remaining regions calculated in such a way are combinedif 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 Standardoption and definethe custom integral region and value in the Rangeand Valueboxes correspondingly.

4.6.4 Bucket Integration

The middle segment of the dialog box for integration options represents a Bucket Integrationfeature 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 beintegrated. You can either set the number of portions (Number of Bucketsvalue) or thewidth of each portion (Width of Bucketvalue). When the Group Treatmentmode is on,Bucket Integration applied to the currently active series will create buckets with the samestarting and final points for all the spectra.

Note The position of every bucket can be manually adjusted in the Group Treatmentmode.

If you are working with a series of spectra, selecting the Intelligent Bucketingoption will calculate the temporary spectrum to which Bucket Integration will beapplied (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 Seriesmenu, chooseTable of Common Integrals.

For the current example, do not enable this option.3. Click OKto apply changes.

Starting from version 10.0, ACD/1D NMR Manager allows you to specify the name and location ofthe .ESP file containing the temporary spectrum of sum or projection (with Intelligent Bucketingapplied) whose integral ranges you want to apply to the current spectral document:

To select a file, either choose it from the File Namelist or click Browse and specify its

name and location in the Select File Namedialog 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 or select all of the integrals and click Delete Selected Integral

Curves .Tip To temporarily hide integral curves, on the General toolbar, release Show Integral

Curves .

2. On the Integration toolbar, clickAuto Integrate . The program automatically integrates

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 segmentaround 4.8 ppm, and then click to select it.

2. In the Reference Integralbox 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 recalculatedrelative to the entered value.

3. ClickAccept 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 orhorizontal) of integral values.

1. From the Optionsmenu, 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 OKto apply the changes and close thedialog 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). Peakparameters can be adjusted during the optimization based onthe Levenberg-Marquardt algorithm

1to provide the best fit of the calculated spectrum to

experimental data points. The Peak Fittingtool finds the most use for resolving overlappingpeaks 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 theprevious sections. Depending on the options you have applied to it when doing theprevious exercises, the peak position may slightly differ from what you will see inthe pictures below.

To enter the Peak Fitting mode, on theAnalysismenu, point to Peak Fitting, and then choose

Enter Modeor, on the Operation toolbar, click Peak Fitting . Note that a new Peak

Fitting toolbar appears.

1William 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), SecondEdition., Cambridge University Press, 1996, pp 678-683.


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4.7.1 Specifying Peak Fitting Options

1. Click Peak Fitting Options to display the corresponding dialog box. The Fitting

tab appears first:

2. In the Default Peak Parametersarea, specify the parameters (peak width and function) thatwill be applied to each peak added to a model. For the current example, set the Widthto 2and Functionto Gauss+Lorentzwith the Lorentz Fraction set to 0.5.

3. In the Limitsarea, restrict any variations in peak widths and positions during optimization.The Fit pointoption allows you to deresolve data during optimization. You can select every2

nd, 3

rd, 4

th, or 5

thpoint 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 everypoint unless the spectrum has excessive resolution.

4. In the Upon Optimizationarea, set up some actions to be done as soon as optimization hasbeen completed: sound beep, show protocol, and/or update the Table of Peaks with adjustedparameters.

Note 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 theControl Panel.

If the Update Table of Peakscheck box is not selected, the results are placed into the PeakParametersdialog box and can only be updated from there. Otherwise, all of the results areautomatically updated when you leave the Peak Fitting mode by clickingAccept

Changes .



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5. Switch to the Viewtab and choose the curve elements to be displayed, as well as the color foreach of them. You can also set the dark region colorcolor for the region outside of the PeakFitting area. Select theAnimate Optimization check box to display the current peak fitting"picture" at each iteration. This creates the animation effect which will allow you to keep trackof the optimization process (however, this slows down the whole process).

6. Specify the options as displayed above and click OK.

4.7.2 Defin ing Region

Now we are going to define the region to be modeled. It is not recommended to apply PeakFitting to the whole spectrum at once since it may take a long time. To show the capabilities ofPeak 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 intoyour work. To temporarily hide these elements, from the View menu, choose IntegralCurvesor 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 sothat 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 beprocessed.



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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, youmay have already noticed that there seem to be a couple of unresolved peaks around3.82 ppm. These unresolved peaks were not labeled and were not included into the fitting

equation. To add them, clickAdd/Remove Peaks , and then click the peak near 3.82

to label it and add it to the model:

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 andclick 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 eachiteration. If the corresponding option has been selected in the Peak Fitting Optionsdialogbox, the Optimization Protocolappears:



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4. Click OKto close it and view the results:

5. Open the Table of Peaks (by clickingShow 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 1DNMR 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 modifypeak 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 ofinterest and drag the peak nodes:

To change peak position andintensity, point to the uppernode of the peak so that thefour-way arrow appears anddrag left or right, up or down.

To change the peak width,point to the side node atpeak half-height so that thetwo-way arrow appears anddrag left or right.

To modify peak shape for peaks with theGauss+Lorentz mixed function, point toany of the nodes at the base of the peak,and then drag up or down. This willgradually change the LF from Gaussfunction (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 atdialog box where you can enterthe required values for the selected peak:

Selecting the Lockcheck box near the parameter will make this parameter unchangeable forboth manual and automated peak fitting. Click OKto save the changes.



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4.7.4.3 Batch Modif ication

You can change the parameters not only for each peak individually but also as a batch within theselected region.

1. Click Parameters to display the following dialog box containing a list of peaks

from the selected region and their parameters:

Note Parameters in this dialog box are always displayed in Hz regardless of the currentview options.

2. To change a specific parameter for all peaks, click in the respective column header (thoughnot all of the columns can be changed this way), then enter the new value in the box. ClickOKto apply the changes.

3. To change only one parameter for a specific peak, double-click the corresponding table cell,and then redefine the value:

4. If you click Update Table of Peaks , the specified parameters will be updated to the Table ofPeaks into the columns marked with an asterisk (*).

5. Click OKto apply the changes and close the dialog box.

6. On the General toolbar, click Show Whole Spectrum .

7. ClickAccept 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 associationscan be made. For example, you can assign peaks or spectrum regions to portions of thestructure, or you can use the information from the structure for defining multiplets.

1. On the Window Switching bar, click ChemSketch to switch to the ChemSketchwindow and make sure that you are in the Structure mode (if not, on the General toolbar, click

Structure ).

2. On the right Reference toolbar, clickACD/Dictionary . If there are any structures in the

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 theACD/Dictionary dialog box are set asfollows:

4. In the Quick Searchfield, enter catechinic acid:

You will see the structure of catechin appear.

5. Click OKto copy the structure to the ChemSketch window and click in the workspace to pastethe structure:

O

OH

OH

OHOH

OH

HH

Note It is recommended to use stereo bonds to draw hydrogens of the CH2groupexplicitly for making the results of the assignment and verification procedures moreevident. 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 theAt tach structure to the current spectrum :

7. Click OK. You are switched to the Processor window, and the structure is associated with thespectrum.

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;