NMRnotebook Documentation - Software1. Drag the horizontal axis to move the spectrum in both directions. Double click to reset the zoom window 2. Drag the vertical axis to move the

NMRnotebook Documentation

Summary

Basic uses p3Importing NMR data p5Organizing your document p7Processing NMR data p8Displaying NMR data 1D NMR datasets p10 2D NMR datasets p12Printing NMR data p18Console p20Core features p21Configuration p22NMRnotebook Interface p23 Menu bar p24

NMRnotebook documentation 2

Basic usesThis is a brief explanation of the basic uses of NMRnotebook

NMRnotebook interfaceThe interface is composed of six parts:

• A menu bar and a toolbar to make and manage your project• A mini map view to explore your 2D spectra• The NMRnotebook document summary• The main spectrum view display and two display control buttons

See section “Reference Manual/User interface” for more details

NMRnotebook documentLike a real notebook the document is composed of several pages. You can mixe together several spectra coming from several experiments and/or spectrometers, to build up your project. The NMRnotebook allows you to manage your project your way: by sample, by user, by date, by NMR experiments, ...

Explore your spectraThe NMRnotebook lets you interactively explore your data:

• Zoom in and out• Move the spectra in all directions• Use the trace zoom window• Change displayed units• Modify the scale factor• And more…

As shown below:


1.Drag the horizontal axis to move the spectrum in both directions. Double click to reset the zoom window

2. Drag the vertical axis to move the spectrum in both directions. Double click to reset the zoom window

3. Click inside to zoom-in. Click outside to cancel4. This trace display the entire spectrum5. Modify the zoom window by dragging its border line6. Drag the zoom window itself to move around the spectrum7. In the display window:

◦ Use the scroll mouse button to modify the scale factor◦ Double click to display the entire spectrum◦ Left click to choose several display options (see section “Reference Manual/User

interface/Display options” for more details)Explore your 2D spectra in the same way.


Importing NMR dataThere are several ways to import NMR data using NMRnotebook.

• Using the icon : This will create a new document containing only the file you've chosen. It behaves like the "File/Open" menu entry.

• Using the icon : This will append the chosen file to an existing document. It behaves like the "File/Add data..." menu entry. Note that this option is only available if a document already exists, which means that you must use the above option for importing the first NMR data into your document.

• By dragging a file into the "Summary area" and dropping it there. It behaves like the "File/Add data..." option presented above.

NMRnotebook recognize automatically the format of the file the user has chosen. It does this by examining the file extension and the content of the directory from which the imported file comes from. Any kind of files can be imported but some of them are really recognized :

• NMR data sets: These files are read and converted to an internal format. They can be displayed and processed. The following formats are supported: Bruker (fid, ser, 1r, 2rr), WinNMR, Varian, Jeol, Gifa, Aspect and SIMPSON (1D). Files that must be imported are:

1. Bruker:■ 1D data sets:

■ name/expno/fid■ name/expno/acqu■ name/expno/acqus■ name/expno/pdata/expno/1r (if you want)■ name/expno/pulseprogram (if you want)

■ 2D data sets:■ name/expno/ser■ name/expno/acqu■ name/expno/acqus■ name/expno/acqu2■ name/expno/acqu2s■ name/expno/pdata/expno/2rr (if you want)■ name/expno/pulseprogram (if you want)

2. Varian:■ name/fid■ name/procpar

3. Jeol:■ old version:

■ name/hdr■ name/bin

■ new version:■ name/jdf

4. Tecmag:name/tnt• Text files: These files are read and are viewed and edited from NMRnotebook.• Image files: They are displayed in NMRnotebook and can be superimposed to displayed

NMR spectra in NMRnotebook.For the other file types, NMRnotebook does nothing except copying them into the current document and calling the appropriate program to view/edit these files. For example, NMRnotebook will launch Excel for files with ".xls" extension and Word for ".doc" files.


Each time you had data to a document, the "fresh" data is appended at the end of the document. The user can move the data into the "NMRnotebook" summary using either :

• Drag & Drop inside the "Summary".• Using the contextual menu (menu that appear when right clicking on an entry in the

"Summary".


Organizing your documentNMRnotebook is not limited to processing / viewing / printing NMR data-sets. It is "report-oriented" and helps the user to create an organized document (called a "notebook") which can be viewed as a report on an NMR study.

Several features are intended to do so :

• "Tree-like" organisation of your document including named sub-directories. Elements can be moved around by drag & drop.

• "Cut & Paste" support for exchanging data between different notebooks.

• Ability to incorporate any type of data into the document. The user is not limited to NMR data but can insert any other relevant document. NMRnotebook takes care to launch the appropriate program to handle properly the documents it doesn't handle itself.

• Easy to use print & graphic export.

• All the pieces making up a study are kept in a single file (a "notebook"). Even if the file grows as big as 250 Mega it is easy to exchange it between users.

• The files ("notebooks") are already compressed in order to keep their size to a minimum. You don't need to compress files.Note that the files are organized according to the OpenDocument format.


Processing NMR dataNMRnotebook allows the user to process NMR FID in three ways :

• Using the icon : This icon starts the "full automatic processing" which will transform the FID into a processed / phased / baseline-corrected / peak-picked and integrated spectrum. This full automatic processing use informations about the FID to choose the best parameters for the processing. For example, the apodisation is chosen depending on the observed nucleus (among other parameters).

The user can customize the automatic processing using a dialog box that appear when

clicking on the "down arrow" on the right of the "gears" .

"Expert processing dialog box"

• The operations performed during this automatic processing can be viewed using the "Audit trail" entry in the contextual menu. It opens a window displaying an HTML file listing

the operations int the order they were performed along with the parameters used.

• Step-by-Step processing using the tools in the "Process" menu : This kind of processing is intended for more advanced users who wan't to gain more control on the

processing. The entries in the "Process" menu are sorted in the logical / natural processing order. The user is free to skip some steps.

For standard NMR FID, using the "full automatic processing" gives the same results that would be obtained by the "Step-by-Step" processing, but with only one mouse click.


"Processing Menu"

• Using the console by writing processing macros : For really advanced users (and mainly spectroscopist using non-standard pulse programs), writing macros can be the

only way to perform the processing. Please refer to the section "Macro Documentation" of this manual for more information.

Using the console will be detailed later in this manual.


Displaying NMR dataDisplaying 1D NMR datasets

Superposition

It is possible to superimpose several 1D NMR spectra as it is demonstrated in the following picture.

"Superimposition of several 1D spectra."

The spectra are superimposed according to the unit of the X axis (which is displayed on the left of the X axis). This unit can be changed by clicking on it, for usual spectra there are 3 valid units : PPM, Hz and point. Usually the unit to use for display / superimpose of spectra is PPM, this is the default anyway...The user can change the way the superimposed spectra are layed out on the screen :

• Using the "red arrow" on the screen by dragging the arrow end. It changes the spacing and slope between the displayed spectra.

• When clicking on one spectrum name, a X-axis graduation appears just above the normal one. This graduation can be dragged around to change the shift.

• Using the menu that appear when right clicking on one spectrum name. This gives access to some auto-alignment options.

The scale of individual spectra can be changed using the mouse-wheel with the mouse positioned of the spectrum name. This is demonstrated on the next picture.




Displaying 2D NMR datasets

Superposition

Like 1D spectra, 2D spectra can be superimposed too. It is useful to detect off-diagonal peaks that are present in one experiment and absent in another which might be helpful for the attribution process.


Using 1D spectra as traces


"1D traces."

Extraction of rows / columns

It is possible to extract rows or columns from the 2D traces. To achieve it first click on the "scissors" which are displayed in the top right corner of a 2D spectrum view. Two dashed lines will appear on the display as on the next picture. These lines can be dragged around using the mouse. During the drag, the corresponding trace (either horizontal or vertical) will be updated to reflect on which row / column the dashed lines are. The dashed lines disappear when the user click on the "scissors" again.


"Dashed lines tells which row / column are displayed in the traces."

To extract a projection and create a new 1D spectra, right click in the trace area, a popup menu should appear, select the last entry "Extract", that's it !


"Trace option menu."

View layouts

By default, NMRnotebook shows only one view which correspond to the most recently imported dataset, result of processing or selected dataset. If the user clicks on the button located in the upper-right corner of the spectrum window, up to four windows will show up. These windows correspond to the last viewed datasets.

It is possible to arrange the windows in 3 different ways :

• Horizontally.• Vertically.• In a 2 by 2 grid.


"Layout menu and windows arranged in a 2x2 grid."

This is useful when using the "correlated cursor" described in the next section.

Correlated cursors

NMRnotebook provides a so-called "Correlated cursor". The "correlated cursor" will be displayed in all the views in which the normal cursor is activated. This "correlated cursor" is really useful when displaying 1D and 2D spectra at the same time, thus enabling to detect 1D peaks involved in a 2D off-diagonal correlation.


"Correlated cursor between 1D and 2D spectra."


Printing NMR dataWithin NMRnotebook it is easy to prepare images and / or to print your spectra. Preparing an

image or printing is done using the icon for both operations. Using the icon will print the displayed spectrum (spectra) using the current preview settings.

NMRnotebook behaves nearly like a WYSYWYG (What You See Is What You Get) program but allows the user to customize the printing a little bit. For example, it is possible to add a frame and a title to the preview.

Instead of printing the spectrum, it ca be exported as an image in various formats including the most popular vectorial and bitmap file formats :

• Bitmap formats : GIF, RAW, PPM, JPEG, PNG.• Vectorial formats : EPS, PS, PDF, SWF, EMF.



ConsoleThe "console" mode in NMRnotebook allows direct manipulation of NMR data. The purpose of this section is to describe how to switch to "console" mode and to transfer an NMR dataset in the console. The section "Macro documentation" documents the commands and the macro language that can be used in the console.

To send an NMR dataset in the console, use the contextual menu that appear when right clicking in the summary. To leave the console double-click on an entry in the summary.

Another way to switch to the console is to use the menu "Macros/console". Doing it this way will not load the console with any data.


Core featuresThe basic version of NMRnotebook allows to process 1D and 2D NMR datasets.

Supported formats

The following formats are supported.

• Bruker XWIN-NMR• Varian• Jeol• Gifa• Aspect

NMR 1D processing features

• Full automatic processing from FID to peak-picked and integrated spectra.• Semi-automatic processing.• Offset correction.• Apodisation (exponential broadening, gaussian boadening, gaussian enhancement, ...).• Fourier transform.• Phase correction.• Baseline correction.• Real part extraction / imaginary part computation.• Peak-picking.• Integration.• J-coupling analysis.• Addition/Substraction of FID / spectra.

NMR 2D processing features

• Full automatic processing from FID to peak-picked and integrated spectra.• Semi-automatic processing.• Offset correction.• Apodisation (exponential broadening, gaussian boadening, gaussian enhancement, ...).• Fourier transform.• Phase correction.• Baseline correction.• Real part extraction / imaginary part computation.• Peak-picking.• Shearing / Tilting.• Symmetrization of 2D spectra.

Graphical features

• OpenGL rendering for maximum performance.• Printing of 1D and 2D FID or spectra.• Graphical export of 1D and 2D FID or spectra in various formats (PostScript, SVF, PDF,

JPEG, GIF ...)• Superposition of spectra in 1D and 2D.

Additional modules• DOSY module.• 1D line-fitting module.• Solid-State NMR module. Still under development.



ConfigurationNMRnotebook is available for computers running on :

• Windows VISTA.• Windows XP / NT.• Mac OS 10.3.9• Mac OS 10.4• Mac OS 10.5• Linux (GLIBC version 2.5 required)

For NMR data rendering, NMRnotebook uses OpenGL and it is recommended to use a computer with a Graphic Card. On some computers without any graphic card the display might be problematic (screen flickers, black screens or filled with garbage ). Even worse, with some Intel Chipsets the program might crash when trying to display an NMR data set (see FAQ for a workaround). Graphic Cards are now affordable (less than 50$ for the cheapest ones which are enough to do the job), most popular brands are Nvidia and ATI. We recommend NVidia GPUs (especially for LINUX users).To feel confortable with NMRnotebook for an everyday usage, we recommend a minimum of 1 Gb of RAM. The processor speed is not as important unless you plan to purchase the DOSY module for NMRnotebook (DOSY processing requires much more computation compared to standard NMR processing).Most modern computers (either towers or laptops) usually fullfill these requirements.


NMRnotebook Interface

The interface is composed of six parts:• A menu bar (1) and a toolbar (2) to make and manage your project• A mini map view to explore your 2D spectra (3)• The NMRnotebook document summary (4)• The main spectrum view display (5) and two display control buttons (6)

Each part is described in detail (please see the sub-trees of the section "User interface")


1. Menu bar

The “Menu Bar” is composed of nine menus and each of them is described in detail (please see the sub-trees of the section "Menu bar")

1.1. File

From the menu bar, click over the “File” button to display the window shown below

Several menus are available and are described in detail below:

• New: To create a new notebook• Open: To open an existing notebook or create a new one and import data in it• Add data…: To import new data into the notebook. Added data will be in the document

summary• Close: To close the notebook• Save: To save current notebook• Save as: To save notebook in an other file format• Notebooks : All open notebooks are listed under this menu as shown below


• Properties…: Properties of the (General, Author and File)• Preview: To preview and define page printing. Permits also to export view to various

graphical formats• Print: To print your result• Quit: To close all active notebook (s) and then quit NMRnotebook

1.2. Edit

From the menu bar, click over the “Edit” button to display the window shown below

Several menus are available and are described in detail below:

• Copy: To copy data from a notebook to an other• Cut: To move data from a notebook to an other• Paste: To paste copied or cut data into the desired notebook• Spectrum Properties: This menu allows you to see the properties of the spectrum

(General, Spectrometer, Time axis and Expert)We will focus only on “times Axis” and “Expert” menus



In “time axis” or in “t1/t2 axis” menu, you will find information about acquisition parameters:

o Axis: It has various kind which depends on the data: Time (FID), Frequency (spectrum), Damping Diffusion (processed DOSY), Damping Relaxation (processed TOSY), DOSY Q2 (DOSY with no processing), Time Relaxation (TOSY with no processing) or Other

o Complex/real: Dataset can be real or complexo Acquisition mode in 1D dataset can be one of these: Simultaneous and

SequentialAcquisition mode in 2D dataset: t1 axis: can be one of these: States, TPPI, States-TPPI, Echo/Antiecho, real, phase modulation, none or simultaneous t2 axis: like in 1D dataset

o Observed nucleus: This menu determines the observed nucleus. If the nucleus is wrong, you can set it correctly

o Carrier frequency (MHz): Larmor frequency of the observed nucleus (e.g. for a Bruker Spectrometer it corresponds to SFO1)


In “expert” menu, you will find information about :



o Zero time position: A non-zero value here is observed for instance when using digital filtering either on the Bruker or on the Jeol spectrometers. The digital filters of the Varian spectrometer don’t generate any first zero points

o Reference offset: This value corresponds the ppm value of the last data

point of the spectrum (the first point on the right of the spectrum)

1.3. Process

Several NMR processing functions are available and can be used to process your dataFrom the menu bar, click over the “Process” button to display the window shown belowEach of these functions are described in detail (please see the sub-trees of the section "Process")


1.3.1. Offset correction

We give an example (1D data) where an offset correction will be applied As shown below, the fid has an offset, as a result it’s not symmetrical about the zero line


Just click the “Compute” button to execute the offset correction

Click the “Compute” button to execute the correctionYou can cancel the current menu with the “Cancel” buttonPress “Validate” to accept the correction The result is shown below and now the fid is symmetrical about the zero line. Note that a child fid

is created (see the document summary (1))


1.3.2. Manual Apodisation

Apodisation (literally means “removing the foot”) is very used in NMR in order to enhance Signal/Noise ratio. It’s sometimes mistakenly called “filtering”. This mathematical operation consist to multiply the signal by a window function. The NMRnotebook offers some window functions (as shown below)

We give an example (1D data) where Exponential Broadening is applied with a 2.3 LB value


If you want to see the effect of this operation, check “FID result” in the Display box. Then the new FID appears like red (as shown below). You can change the LB value and see how it modifies the signal


Press “Validate” to store the result (the red FID) into the NMRnotebook document summaryYou can exit from the “Apodisation” menu without saving any changes by clicking on “Cancel

1.3.3. Zero filling

Manual zero filling can be done in the NMRnotebook. We will applied a zero filling (add zero point to the spectrum). The original spectrum’s size is 2048

points


The size values can be set in two ways:

(i) use the arrow buttons(ii) enter a value manually in the box “0-filling size”

Click the “Compute” button to execute computationYou can cancel the current menu with the “Cancel” buttonPress “Validate” to accept the computation


1.3.4. Fourier Transform

A Fourier Transformation is a mathematical processing which converts a time domain signal to a frequency domain signal. The Fourier transform algorithm depends on spectrometer and acquisition scheme The “Fourier Transform” window is composed of three parts:

• FT algorithm1D data: the algorithm can be Simultaneous, Sequential, Complex FT or Real FT2D data: For the indirect dimension (F1): the algorithm can be States Haberkorn, TPPI, States Haberkorn+TPPI, Phase modulation, Echo-Antiecho, Complex FT or Real FT For the direct dimension (F2): the algorithm can be Simultaneous or Sequential

• Modulus PreviewThe window reflects the result (in modulus mode) of applying the FT algorithm

• OptionsYou can reverse the spectrum (see also the next part) and change its sizeFor 2D data you have two other options “Invf on F1” and “Modulus”. The first one inverses imaginary part of the F1 dimension's data (if complex). The second takes the complex modulus of the spectrum



Press “Validate” to store the spectrum into the NMRnotebook document summaryYou can exit from the “Fourier Transform” menu without applying any Fourier transformation by clicking “Cancel”

1.3.5. Reverse spectrum

This menu allows you to reverse the spectrum. It’s available for 1D and 2D dataset. For a 2D spectrum, the overturn ca be done in both dimensions F1 and F2 (Choose axis box)Click the “Compute” button to reverse the spectrum. Press “Undo” to erases the change done to the spectrumYou can cancel the current menu with the “Cancel” buttonPress “Validate” to accept the computation


1.3.6. Phase Correction

This menu allows you to change manually the spectrum phasePhasing the spectrum involves correcting two parameters: zero-order phase, which is frequency independent; and first-order phase, which is frequency dependent

Note that you can phase correct your spectrum by using from the toolbar


1D phase correctionWe give an example of 1D phase correction

To visualize and modify the phase correction you can use (as shown below):

• The “0 order” and “1st order” boxes (1) to enter a value manually• The arrow buttons (2)• The scroll wheel (3)• The scroll mouse

The values of phase correction can be changed in two modes: “Fine” and “Coarse”. The values change by tenth and by one respectivelyThe red line is the pivot. By default, it's placed on the largest peak. It presents the single frequency where the first order phase correction has no effect.When the mouse pointer is positioned over the pivot:

(i) hold down the right (or left or scroll) mouse button and move the mouse to put the pivot where you want

(ii) click the left mouse button, “Pivot Options” window (4) will appear (as show below)


You can reset the phase values with the “Reset” buttonPress “Validate” to accept the phase correction To phase correct your spectra you can follow these steps:

• correct the zero-order phase• Then (if it’s needed), move the pivot on the desired peak and correct the first-order phase

2D phase correction In the Phase 2D menu, click on “F1” (or “F2”) to phase correct the 2D spectrum in the indirect dimension F1 (or in the direct dimension F2). Then select a column (or a row) which will be corrected. The phase correction is identical to 1D phase correction (see above) To visualize the result of your phase correction, click the “Apply to 2D” button or check “Auto” for automatic visualization


1.3.7. Baseline CorrectionThe NMRnotebook offers some options in order to correct a curved baseline (as shown below)The correction can be done in three different modes: “Spline”, “Fit polynomial” and “Moving average”

As shown below we applied the “Spline” mode to correct the spectrum’s baseline In this mode, a red vertical line (1) is displayed. It allows you to add pivot (2) by right clicking with your mouseCheck “Spectrum result” to display the correction’s resultPress the “Remove All” button to remove all pivots You can cancel the current menu with the “Cancel” buttonPress “Validate” to accept the correction


Below, we show the result of the different modes. In this example the different modes give the same result.User can try each of them and choose the best one


1.3.8. Real part extraction

1D dataset can be either real or complex. And on 2D dataset, each dimension can be either real or complex. It’s depends on detection modeThis menu allows you, when your dataset (spectrum) is complex, to extract its real part Click the “Compute” button to execute the extraction. With a 2D dataset, the extraction ca be done in one or both dimensions F1 and F2 (Choose axis box)You can cancel the current menu with the “Cancel” buttonPress “Validate” to accept the extraction


1.3.9. Imaginary part computation

This menu will create a complex spectrum from a real one. If the spectrum (or the dimension of a 2D dataset) is complex, the existing imaginary part will be replaced by the computed one. Click the “Compute” button to calculate the imaginary part. With a 2D dataset, the computation ca be done in one or both dimensions F1 and F2 (Choose axis box)You can cancel the current menu with the “Cancel” buttonPress “Validate” to accept the computation


1.3.10. Spectrum shift

This menu allows you to shift the spectrum. It’s available for 1D and 2D dataset. The shift values can be set in “ppm” or “Hz” unitClick the “Compute” button to shift the spectrum. For a 2D spectrum, the shift ca be done in both dimensions F1 and F2 (Choose axis box)Press “Undo” to erases the change done to the spectrumYou can cancel the current menu with the “Cancel” buttonPress “Validate” to accept the computation


This tool is very useful when you have a 2D spectrum with aliased (or folded) peaks in the indirect dimension (F1)

Example:

We give an example, where Spectrum Shift is applied with a 32 ppm shift value to a 2D 3QMAS 23Na spectrum of the Narsarsukik compound. The spectrum was recorded at 105.892 MHz (9.4 Tesla) with sample spinning at 12.5 kHz The spectrum (as shown below) reveals three frequencies:

• one sodium site Na1 (as expected)• two spinning sidebands in the F1 dimension, SSB1 and SSB2

Their chemical shift observed in the F1 dimension is: 7.14 (Na1), -25.14 (SSB1) and -42.73 ppm (SSB2) The SSB1 is spaced at the sample spinning frequency from the sodium peak (Na1). It’s not the case of the SSB2, so it’s an aliased spinning sideband


When we shift the spectrum in the F1 dimension by 32 ppm, all peaks are moved. Moreover, only the chemical shift of SSB2 is changed from -42.73 to 40.41 ppm and the two others are kept unchanging. Now, the SSB1 and SSB2 are spaced at the sample spinning frequency from the sodium peak Na1 (as shown below)


1.3.11. 2D Symmetrization

The symmetrization can be performed on the current 2D data. It’s allows you to remove unwanted t1 noise (lines of noise that run parallel to the F1 axis). Three types are available: COSY, JRES and INADEQUATE. Available algorithm are : mean, min and continuous (not for JRES)


Click the “Compute” button to symmetrize the spectrumPress “Undo” to erases the change done to the spectrumYou can cancel the current menu with the “Cancel” buttonPress “Validate” to accept the computation

We give an example of 2D symmetrization realized on JRES dataA JRES spectrum shows symmetrical frequencies about a horizontal line located in the middle of the spectrum (as shown below)


The symmetrization removes artifacts (as shown below)


1.3.12. 2D Projections

The 2D spectrum is usually plotted with its 1D projections for clarity (see Traces in the “Display Options/Display Parameters” section)Suppose we have a 2D spectrum. If we process it (Phase correction, Baseline correction,…), then the 1D projections will change. Unfortunately, the old 1D projections are kept. To see the new 1D projections we must recalculate them by using this menu Skyline and/or Mean projections along the F1 and/or F2 dimension can be calculated


Click the “Compute” button to calculate the projectionsYou can cancel the current menu with the “Cancel” buttonPress “Validate” to accept the computation

1.3.13. Shearing…The shearing transformation is very used in NMR in order to change the representation of a spectrum

Click over “Shearing…” button to open the module

This window (shown below on the right) will appear. Four shearing transformations (as shown below on the left) are available:

• An experiment performed in the SECSY (Spin Echo Correlated Spectroscopy ) mode is transformed into the COSY (Correlation Spectroscopy) representation

• An INADEQUATE (Incredible Natural Abundance Double Quantum Transfer Experiment) spectrum is transformed into the COSY representation


• MQMAS (Multiple Quantum Magic Angle Spinning)/STMAS (Satellite transition Magic Angle Spinning): 2D MQ/SQ and 2D ST/CT correlation spectrum are changed to a 2D isotropic/anisotropic correlation spectrum

Note that others transformations can be made by using the “Custom shearing”

We will focus on “STMAS-MQMAS shearing” and “Custom shearing” transformation by giving processing examples

1.3.13.1. STMAS-MQMAS ShearingAs shown below, we create two folders called ALPO40-MQMAS and Berlinite-STMAS in the NMRtec folder (itself stored in our hard disk d).In each created folder we store the folders both named 1 which contain experimental data acquired on a Bruker spectrometer and are imported from the spectrometer's data directory. They correspond to a two-dimensional (2D) 3QMAS Z-filter experiment of ALPO4-40 compound and 2D STMAS Z-filter experiment of Berlinite compound respectively. In both experiments, the aluminium-27(with half-integer spin 5/2) is the detected nucleus


With our software, we create a new notebook called STMAS-MQMAS-shearing and we save it in the NMRtec folder. Then we import (see the “Import” section) form each folders 1 the files named SER into this created notebook .

As shown below, in the document summary (see the “Document Organization” section) the names of data show that the observed nuclei in the indirect-dimension are Gallium-71 and proton. It’s a mistake but this is a normal behavior. Indeed, the nucleus in the indirect-dimension has not been set when data has been acquired on the spectrometer

This mistake can be easily corrected in the “Dataset properties/t1 axis/Observed nucleus” (see the “Edit” or the

“DocumentSummary” section)

The two data are processed (FT, Phase correction, Apodisation) to obtain unsheared 2D spectra (as shown below)

ALPO40-MQMAS 1:

The 2D MQMAS unsheared spectrum is shown below


As shown below, we

select from the Shearing menu:

1. STMAS-MQMAS shearing

2. Experiment type is set to MQMAS

3. In this example, Spin is 5/2

4. Coherence │pq│-Shearing slope are 3Q and 19/12

Recall that in this example, the studied nucleus and the desired coherence are 5/2 and 3Q respectively. But the others quadrupole nuclei with a half-integer spin (3/2, 7/2 and 9/2) and their MQ coherences are also available


Click the “Apply” button to shear the spectrum. Press “Undo” to erases the change done to the spectrum

You can cancel the current menu with the “Cancel” button

Press “Validate” to accept the transformation

Note that the shearing transformation and the scaling of the indirect axis (F1) are done simultaneously. This labeling is necessary to extract chemical shift and quadrupolar NMR parameters from 2D MQMAS spectra

As you know, several conventions [1-6] for labeling the F1 dimension exist in the literature. At the moment, with our software, the scaling is done according to the convention introduced by J.-P. Amoureux and C. Fernandez [3, 4]. The others conventions will soon be provided.

The 2D MQMAS sheared spectrum is shown below


In the NMRnotebook, the carrier frequency (in MHz unit) of the F1 dimension is defined according to:

carrier frequencyF1 = │k1│x carrier freaquencyF2 with k1 = k - p

The values of k1 and k (shearing slope) for the four half-integer quadrupole spins I and the coherence order p are reported in Table 1


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(1) MEDEK A., HARDWOOD J.S. and FRYDMAN L., "Multiple-quantum magic-angle spinning NMR: a new method for the study of quadrupolar nuclei in solids". J. Am. Chem. Soc., 117 12779-87 (1995).

(2) BODART P.R., PARMENTIER J., HARRIS R.K. and THOMPSON D.P., "Aluminium environments in mullite and an amorphous sol-gel precursor examined by 27Al triple-quantum MAS NMR". J. Phys. Chem. Solids, 60 223-28 (1999).

(3) AMOUREUX J.P. and FERNANDEZ C., "Triple, quintuple and higher order multiple quantum MAS NMR of quadrupolar nuclei". Solid State Nucl. Magn. Reson., 10(4) 211-23 (1998).


(4) AMOUREUX J.-P. and FERNANDEZ C., "Erratum to "Triple, quintuple and higher order multiple quantum MAS NMR of quadrupolar nuclei" [Solid State NMR 10 (1998) 211-223]". Solid State Nucl. Magn. Reson., 16 339-43 (2000).

(5) MASSIOT D., TOUZO B., TRUMEAU D., COUTURES J.P., VIRLET J., FLORIAN P. and GRANDINETTI P.J., "Two-dimensional magic-angle spinning isotropic reconstruction sequences for quadrupolar nuclei". Solid State Nucl. Magn. Reson., 6 73-83 (1996).

(6) MILLOT Y. and MAN P.P., "Procedures for labeling the high-resolution axis of two-dimensional MQ-MAS NMR spectra of half-integer quadrupole spins". Solid State Nucl. Magn. Reson., 21(1/2) 21-43 (2002).

---------------------------------------------------------------------------------------

Berlinite-STMAS 1:

The 2D STMAS unsheared spectrum is shown below. Recall that in this example, the studied nucleus is 5/2. The spectrum shows two resonance: CT-CT (central transition) and CT-ST1 (satellite transition )

As shown

below, we select from the Shearing menu:


1. STMAS-MQMAS shearing

2. Experiment type is set to STMAS

3. In this example, Spin is 5/2

4. Satellite Transition-Shearing slope are ST1 and 7/24

The others quadrupole nuclei with a half-integer spin (3/2, 7/2 and 9/2) and their satellite transitions are also available

Click the “Apply” button to shear the spectrum. Press “Undo” to

erases the change done to the spectrum



As for MQMAS, the shearing transformation and the scaling of the indirect axis (F1) are done simultaneously. The scaling is done according to the convention introduced by J.-P. Amoureux et al [7]

The 2D STMAS sheared spectrum is shown below


In the NMRnotebook, the carrier frequency (in MHz unit) of the F1 dimension is defined according to:

carrier frequencyF1 = │k1│x carrier freaquencyF2 with k1 = k - 1

The values of k1 and k (shearing slope) for the four half-integer quadrupole spins I and satellite transition are reported in Table 2


---------------------------------------------------------------------------------------

(7) AMOUREUX J.P., HUGUENARD C., ENGELKE F. and TAULELLE F., "Unified representation of MQMAS and STMAS NMR of half-integer quadrupolar nuclei". Chem. Phys. Lett., 356(5-6) 497-504 (2002).

---------------------------------------------------------------------------------------

1.3.13.2. Custom Shearing

You can also easily do a shearing transformation by using the “Custom shearing”

Here an example where the “Custom shearing” is used to shear the 2D ALPO40 MQMAS 1 spectrum (see the “STMAS-MQMAS” section):

By default, the coordinates pivot (graduated circle (1)) are 0.5 and 0.5. But it can be positioned any place:

(i) By using the arrow buttons or the scroll wheel (2)

(ii) Or, position the mouse pointer over the pivot then hold down the right (or left or scroll) mouse button and move the mouse to put the pivot where you want

The slope values can be set in several ways:


(i) By using the “Slope” box (3) to enter a value manually

(ii) By using the arrow buttons or the scroll wheel (4)

(iii) By right clicking over the pivot

Change the values of the slope moves the green line (5). In this example the slope takes this value: 57.7° (= Arctan(19/12), see Table1)

Note that no labeling is done to the F1 dimension

Click the “Apply” button to shear the spectrum. Press “Undo” to erases the change done to the spectrum



1.4. AnalysisNMRnotebook documentation 66

Several NMR analysis tools are available and can be used to process your data

From the menu bar, click over the “Analysis” button to display the window shown below

Each of these tools are described in detail (please see the sub-trees of the section "Analysis")

1.4.1. Peak Picking

The NMRnotebook can do a complete automated peak picking (PP). As shown below, peak picking can also be done by the user


Peaks can be either added or deleted one by one or by region.

• Single peakWhen you click with your mouse over the “Single peak” button, a vertical red line (1) is displayed.Place this line where you want and then left click (or middle) to add a peak

• By zoneHold down the right mouse button (also the left or the middle one) and draw a zone (2). Then click inside it. You can do these two step by using either the left mouse button or the middle one


Press “Validate” to accept the peak picking

Note that you can add peak(s) by using either the icon from the toolbar or the display options (see section “5.4.1”)

When you press “List Peak…” a window which contains a list of peaks (if they exist) will be displayed (see section “1.4.5”)

1.4.2. Integration…NMRnotebook documentation 68

This analysis is only available for 1D spectra

The NMRnotebook can do a complete automated integration analysis. It can also be done manually by the user

In the example below, we will talk about all tools available in this menu.

Integrals were added manually (we right click into an empty area beside the spectrum, see section “5.4”)

Note that the spectrum is well phased and a baseline correction was applied. These corrections are necessary before starting any integration

From the panel "1D Integral", user can control the tools display:

(i) Integral layer: all tolls are hidden when this checkbox is unchecked

(ii) Informations (1): By default, this checkbox is unchecked. Informations are displayed when the cursor is placed over the integral

(iii) Patern: if it’s unchecked, Correction (2), Shift Y (3) and Auto Scale View are hidden

(iv) Color spectrum (4): if it’s checked, the spectrum is colored in red

As shown below, user can define the appropriate regions in three different ways: (5), (6), (7) and (7’)

Place the cursor over one of these points. Then hold down the right mouse button (also the left or the middle one) and move the cursor to define the integral region

Several options (8) are available. To display them, place the cursor over one of these points (1, 3, 5, 6, 7 or 7’) and left click your mouse

Press “Calculate” to calculate integrations or “Reset” to do a reset


Press “Validate” to accept the integration


1.4.3. Import Peaks...

This menu is very useful and allows you to import peaks from a spectrum to an other one. It’s available for 1D and 2D spectra

We give an example where peaks are imported form spectrum 1 to spectrum 2

As shown below, the first one is obtained with an automated peak picking and the second one has no peak picking

Note that peak(s) can be imported only from spectra which are contained in the same notebook.


Now peaks

will be imported from spectrum 1 to spectrum 2 (1). In this example, the notebook contains only two spectra

Click the “Import” button to import peak(s)

You can delete all peaks with the “Clear” button

Press “List Peak…” to display the list of peaks

Press “Validate” to accept or “Cancel” to cancel the current menu


1.4.4. Import Annotations...

This menu is very useful and allows you to import peaks from a spectrum to an other one.

We give an example where annotation is imported form spectrum 1 to spectrum 2

As shown below, only the first one contains annotation ‘Import annotations”

Note that annotation(s) can be imported only from spectra which are contained in the same notebook.

Now annotation will be imported from spectrum 1 to spectrum 2. In this example, the notebook contains only two spectra

Click the “Import” button to import annotation(s)

You can delete all annotations with the “Clear” button

Press “Validate” to accept or “Cancel” to cancel the current menu


1.4.5. List Peak...

Use this menu to display and/or to print the list of peaks (if they exist in the spectra)

This list can be exported into txt or MS xls format


1.4.6. List Integral...

Only available for 1D spectra

Use this menu to display and/or to print the list of integrals (if they exist in the spectra)

This list can be exported into txt or MS xls format

1.4.7. Line Fit

Numerical simulations have become an indispensable part of modern day research

Numerical simulations are very used in modern day research

The NMRnotebook provides a powerful tool to fit NMR 1D spectra

We give an example where a spectrum is fitted. The studied compound is the Quinine

Note that the peak picking must be done before using this module

From the panel "Line fitting", three types of ray can be added: Lorentzian “L”, Gaussian “G“ and Mixte “LG”

By default, the width’s line is 2.5 Hz but it can be set in two ways:


(i) use the arrow buttons

(ii) enter a value manually in the box “Width(Hz)”

(iii) enter a value manually in the box “Line-Width(Hz)”, when this part is active (shown later)

Now we will start by adding lines (use the “Add LineShapes” button). In this example thirteen Lorentzian lines (2.5 Hz) will be added

If the spectrum contains large lines, you must change this value

As shown below, the added lines, the synthetic spectrum (the sum of all added lines), the real spectrum and the difference between these spectra are plotted in red, blue, green and black respectively


We will talk about how to control added line(s). Amplitude, position and L/G ration can be changed

For clarity we will present only one line

As shown below, the original line and modified lines are on the left and on the right respectively

The control points are indicated on the original line. Place the cursor over them then hold down one of the mouse buttons (the right one, middle or left) and move the mouse.

Below, the parameter which has been changed:

(a) Position

(b) Amplitude. This parameter is also controlled by the scroll mouse button

(c) L/G ratio (=1 Lorentzian and =0 Gaussian)


Now, press the “Fit” button to compute the fit. Note that only the zoomed region is fitted

The result shown below is obtained instantaneously (the computation is extremely fast !!)


The green spectrum called “Difference” can be moved vertically. To do this, place the cursor over the (its colour becomes red ). Then hold down the right mouse button (also the left or the middle one) and move the cursor.

When you left click over the , theses options will be displayed. As shown below, you can save either “Difference spectrum” or “Synthetic spectrum”

The saved spectrum will be added into the document summary (see section “4”)

Others options are available. To display them, place the cursor over one of the red lines and press the left mouse button. As shown below, the “sum” (“Synthetic spectrum” ) and “residue” (“Difference spectrum”) can be either shown or hidden

In the box called “Line Shapes”, the selected parameters (Amplitude, Position, Line-Width) are taken into account in the computation. The others (phase and L/G ratio) are not

Note that for each parameters, you can change its value by entering manually in its box a new value. Left click into a cell to display these options:

1.4.8. Follow peak or integral value...

This tool is very useful in comparative studies. It allows you to follow the value of a column or an integral cross

It’s available for 1D spectra (only when 1D spectra are superposed) and 2D spectra


Follow peak value:

We give an example with three 1D spectra but the tools works the same for 2D spectra

In this example, spectra 1, 2 and 3 are superposed. Note that a red horizontal line (1) is displayed. It will be used to follow the intensity at a defined position

When you place the cursor on this line, it becomes bold

As shown above, we place the cursor at the position marked by X and we double right click to extract values. The window shown below (1) will be displayed

It contains intensity’s value at this position and for each spectra

User can add text (2) is he wants

Press “Save” to store the list in txt format and “Close” to close this window


Follow integral value:

Follow integral value works as follow peak value. It differs by the necessity to define a region (from a to b)

To do this, place the cursor at the start point (a) and hold down the right mouse button (also the left or the middle one). Then move the cursor until the finish point (b)

To display the list, double right click into this region


1.4.9. J-coupling analysis

The NMRnotebook provides an automatic J-coupling analysis (using AUJ “Automatic J” algorithm from JM. Nuzillard [1])

We give an example where the J-coupling is analysed. The studied compound is the Quinine

As mentioned in the “J-Coupling” panel, for computing J values of a multiplet you must zoom around it, then press the “Compute” button

As shown below, the label is displayed when the cursor is placed at the position marked by X.

This label is composed of two parts:

(1) The chemical shift at the center’s multiplet

(2) This part is itself composed of two parts: the nature of multiplicity (2') and all J-Coupling values (2''). Constant “J” are expressed in Hz

Note that values are decreasing from top to bottom: 17.2 (a), 10.3 (b) and 7.5 (c)

Place the cursor at the position marked by X1, X2 and X3 to display these values

From left to right, these options are displayed when you left click at the position X, (X1 or X2) and X3 respectively

Note that relative intensity ratios (given by Pascal's triangle) will be displayed if you check “Theory peak”


Press the “Simplify” button to remove the smallest value

The results computation can be can be copied (in the clipboard) or saved (in HTML or RTF format) according to the convention of some scientific journals: J. Org. Chem., J. Am. Chem. Soc., J. Nat. Prod. and Tetrahedron. The number of equivalent H atoms can also be indicated


Press “Validate” to accept the computation

---------------------------------------------------------------------------

(1) PROST E., BOURG S. and NUZILLARD J.-M., "Automatic first-order multiplet analysis in liquid-state NMR". C. R. Chim., 9(3-4) 498-502 (2006).


1.5. DOSY

The “DOSY” is an optional module. It is not available with demo version for example

In this section, we describe the processing DOSY spectra with NMRnotebook. This processing is based on the inverse Laplace

transform approach performed by Maximum Entropy

The processing is performed as follows:

STEP 1: Importing data

We create a new notebook called DOSY-Example and we save it. Then we import the experimental data (see the “Using NMRnotebook / Importing NMR Data” section)

Data was acquired on a Bruker spectrometer and a standard DOSY pulse sequence was used. Thirty gradient strengths were applied with 8192 complex data points for each of them. The sample is a mixture of: HDO, glucose, ATP and SDS

As shown below, imported data is well recognized as DOSY data. Note that to perform this importing, the file called “difflist” is required (this is true only for “Bruker” users).


STEP 2: F2 processing

A “full automatic processing is performed by clicking on the gear box

The processing parameters can be modified by clicking either on or on (from the “DOSY” menu)


At this stage, you want to optimise the processing:

(i) correct phase imperfections (see section “1.3.6”)

(ii) careful baseline correction (see section “1.3.7”)

…

STEP 2: F1 processing “ILT processing”

From the “DOSY” menu, click on “DOSY F1 processing”

The window shown below will be displayed

First, choose the number on columns to process


(i) the red lines indicates the threshold used for selecting the columns to process

(ii) is the line is too low, the columns with a signal/noise ratio too low will be ignored anyhow

Second, calibrate your sequence parameters by clicking on

These parameters are extracted from the acquisition parameters and should be ok, however, errors may appear and can be corrected here

(i) Sequence is the sequence type, and can be chosen from the list proposed:

· ste : the standard stimulated echoe sequence

· bpp_ste : ste with bipolar gradient pulses

· ste_2echoes : ste compensated for convection

· bpp_ste_2echoes : bpp_ste compensated for convection

· oneshot : the oneshot sequence from Pelta, Morris, Stchedroff, Hammond, 2002, Magn.Reson.Chem. 40, p147


(ii) nucleus: the nucleus on which the diffusion gradients took place (usually 1H)

(iii) gradient length: (little delta) the total duration of the diffusion gradients (the double of the elementary gradient when bipolar gradients are used)

(iv) intergradient delay: (big Delta) the delay between the coding and decosing gradients

(v) gradient recovery delay: the short delay applied after the gradient before applying any other action, to recover from field fluctuations

Wrong values here means usually that you are using a unusual or modified pulse sequence

The gradient table thumb gives the value in G/cm of the gradient list. These values are computed from the acquisition parameter and cannot be changed from here

Wrong values here means usually a wrong or unusual calibration set-up of the spectrometer.


Third:

This sub-menu permits to choose the diffusion window as wel as the processing level.

Diffusion parameters are given in micron²/sec (10-12 m²/sec). The program estimates the values from the acquisition parameters. It is usually useless to widen the window, but may be interesting to reduce the window to the value present in the data-set

Reducing too much the window to the point that actual signal are not in the processing window will reduce the accuracy of the result

A processing with the value 5 will give you the best results, may the processing time can become quite long if many columns are to be processed

The button Start, will start the processing at once on the computer

The button Save will create a set of files permitting an independent processing, for instance using the XXX macro provided with 2.6 release

Processing time will vary, depending on the processing level and the complexity of the spectra, but usually ranges from less than a second to a minute per column


Finally:

When the computation is launched, a small window allows to follow the computation. NMRnotebook is still reactive, but no other computation should be launched at this stage


At the end, you get the result: computation took 2250 seconds on my laptop - as found in the Audit trail

You will have to compute the projections if required

You can recognize the 4 solutes (lightest - HDO - on the top; heaviest - SDS micelles- on the bottom ). ATP is here around 290 micron²/sec

-----------------------------------------------------------------------------

At this stage, the DOSY processing is completely done and the Diffusion coefficient can be extracted from the 2D DOSY spectrum.

Note that if you have the new version of NMRnotebook (2.6), you can do more, as mentioned above.

Since NMRnotebook Version 2.6

Since this version, several macros were developed which perform new functionalities.

With the “DOSY” module (which is an optional module), you can use these macros: “extract2D”, “DOSYto1D” and “DOSYtoMW”. Each of them is described below.


(A) “extract2D”, use this macro to limit the computation to only one spectral region, thus accelerating the processing time

(B) “DOSYto1D”, you can extract quite faithful 1D spectra :

Simply draw a line for each species to be analysed (see section “5.4.5”)

you will be prompted for the "radius" that will be used for the local projection used to compute the 1D spectra

Here it gives:


(C) “DOSYtoMW“, you can estimate the molecular weight of each species using the fractal dimension method, "NMR measure of Translational Diffusion and Fractal Dimension. Application to molecular mass measurement." Augé, Sophie; Schmit, Pierre; Crutchfield, Christopher; Islam, Mohammad; Harris, Douglas; Durand, Emmanuelle; Clémancey, Martin; QUOINEAU, Anne-Agathe; Lancelin, Jean-Marc; Prigent, Yann; Taulelle, Francis; Delsuc, Marc (2009) The Journal of Physical Chemistry -in press-

Simply draw a line (see section “5.4.5”) for each species to be analysed, and a line for the reference molecule (here HDO)

Then launch the macro:

1. Choose current molecular family:

The window shown below (right) allows you to choose the molecular family. The available list is shown (on the left)

In this example we choose “Small Organic Molecules”


2. Choose current solvent:

The window shown below allows you to choose the solvent (Chloroform or Water)

Then a dialog box shows the reference molecule

3. The result is displayed in a dialog box


This result is not too bad, considering that:

glucose is 180 (found : 210 +/- 77) and ATP is 507 (found : 650 +/- 243)

SDS value is irrelevant here because, being aggregated in micelles it cannot be considered as a "small organic molecule" here.

With this version, the following conditions are available :

(i) Molecule : PolyMethylMetacrylate - PMMA

Conditions - solvent : Chloroform, Temperature : 300.0 K, reference : TMS, Masses between 24300 and 1577000 (range 1.81)


Conditions - solvent : Acetone, Temperature : 300.0 K, reference : TMS, Masses between 24300 and 1577000 (range 1.81)


(ii) Molecule : PolyEthyleneOxyde - PEO / PEG



Conditions - solvent : Water, Temperature : 300.0 K, reference : HDO, Masses between 106 and 847000 (range 3.90)

(iii) Molecule : Linear saturated alcanes

Conditions - solvent : Toluene, Temperature : 300.0 K, reference : Toluene, Masses between 114 and 366 (range 0.48)

(iv) Molecule : Small Organic Molecules



(v) Molecule : Globular Proteins

Conditions - solvent : Water, Temperature : 300.0 K, reference : Tris, Masses between 4190 and 120000 (range 1.45)

(vi) Molecule : OligoSaccharides


(vii) Molecule : Polystyrene - PS



Conditions - solvent : THF, Temperature : 300.0 K, reference : TMS, Masses between 30300 and 3065000 (range 2.00)

Conditions - solvent : THF, Temperature : 300.0 K, reference : TMS, Masses between 580 and 30300 (range 1.72)



Conditions - solvent : Toluene, Temperature : 300.0 K, reference : Toluene, Masses between 370 and 316500 (range 2.93)

(viii) Molecule : Denaturated peptides

Conditions - solvent : Water, Temperature : 300.0 K, reference : Dioxan, Masses between 1899 and 26664 (range 1.15)

Range is log10(maxMW/minMW)

1.6. Macros

This section contains several examples of macros. For more details about macro commands see the “Macro documentation” section

As shown below, we create the folder called NNBMACROS in your home folder (itself stored in our hard disk)

We start the NMRnotebook and we create a new notebook (if you have an existing notebook , you can open it)

From the Macros menu we select Console(beta) and as shown below a "console" will open

In the section (1), you can either type directly macro commands or load them from an existing file (“xxx.py”, “xxx.txt” or “xxx”)

Note that file in “.py” format can be opened with your favorite text-editor

Several buttons are available and their function are described below:

• New: To create a new macro file• Open…: To open an existing macro file• Save: To save current file• Save as: To save current macro in an other file• Run: To run macro commands. When the Blue color of Run has disappeared,

the running is finished.The processed data and the result are displayed in the window on the top (2)

• Store Data: To store the result which will be added in the document summary (3)

• Close: To close the consoleExamples are given in the sub-tree of the Macros section


1.6.1. Example 1: Serial

In this example, we will show how to import a series of 1D data and how to process them

The obtained spectra will be stored in the current notebook

As shown below, we create a folder called Example1-Serial. In this created folder we store the folders named 1, 2, …,6 which contain experimental data acquired on a Bruker spectrometer and are imported from the spectrometer's data directory. They correspond to a one-dimensional (1D) single pulse experiment of xxx compound. In all experiments, the lithium-7(with half-integer spin 3/2) is the detected nucleus

We also store the file called “Example1-serial.py” which contains macro commands. Then we create a new notebook called “Console-Ex1-Serial”

We start by opening the “Example1-serial.py” file. As shown below, “File” (1) indicates where the file is stored on the computer


Macros commands are shown and explained below:

Commands:

1. rootdir = "D:/NMRtec/Macros-Console/Example1-Serial/"

2. ni=1;

3. nf=6;

4. for i in range(ni,nf+1):

5. data=NNB.importData( rootdir + repr(i) + "\\fid")

6. NNB.renameData(data, "serie " + repr(i))

7. putSpectrum(data)NMRnotebook documentation 98

8. em(1)

9. revf()

10. ft()

11. apmin()

12. child = NNB.storeData(data)

13. ax = child.getNNB_NMR_Spectrum().getAxisF(1)

14. ax.setDomainType(1)

15. NNB.renameData(child, "proc " + repr(i))

Discussion:

1. Into the variable “rootdir”, we store the location of folders: 1,2,…,6

2. The variable “ni” indicates the number of the first folder which will be opened

3. The variable “nf” indicates the number of the last folder which will be opened

4. Iteration through the list of folders. The length of the list is 6 (6+1-1)

5. Experimental data “.fid” are imported from each folder and stored into the variable “data”

6. Imported data are renamed as follow: “serie i” (with i=1, 2, …,6)

7. The content of “data” is stored in the buffer

Lines 8, …, 11 are processing commands of experimental data

8. em(1): Multiply data by an exponential: “exponential broadening”

9. revf(): Centering of data.

10. ft(): Fourier transformNMRnotebook documentation 99

11. apmin(): Automatic phase correction

12. Processed data (spectra) are stored into the variable “child”. Itself stored in the current notebook

13. All properties of spectra are stored into the variable “ax”

14. The type of the property “time Axis” (see section “1.2”) is set to “frequency”

The table below give the argument’s value of the function "setDomainType(x)" and its corresponding type “time Axis”

15. Spectra are renamed as follow: “proc i” (with i=1, 2, …,6)

Result:

We click “Run” to execute these macro commands. The console is automatically closed when the running is finished

As shown below, all experimental data were imported, processed and stored in the notebook “Console-Ex1-Serial”


1.6.2. Example 2: Extract Rows

In this example, we will show how to extract rows from a 2D spectrum

Extracted rows will be stored in the current notebook

As shown below, we create a folder called Example2-Extract-Rows. In this created folder we store the folder named JRES-Lasalocid which contain experimental data acquired on a Bruker spectrometer. These data are imported from the spectrometer's data directory. They correspond to a two-dimensional (2D) JRES experiment of “Lasalocid” compound

We also store the file called “extract-rows.py” which contains macro commands. Then we create a new notebook called “Extract-Rows”

We start by importing experimental data “ser”. A 2D spectrum is obtained by using an automatic processing

Then we open the console and the “extract-rows.py” file

As shown below, “File” (1) indicates where the file is stored on the computer



Commands:

1. data=NNB.loadCurrentData()

2. axis = data.getNNB_NMR_Spectrum().getAxisF(2)

3. nuc = axis.getNucleus()

4. sw = axis.getSpectralWidth()

5. off = axis.getCalibrationOffsetPpm()

6. frq = axis.getCarrierFrequency()

7. if ( get_itype_2d() >= 2 ):

8. real("F1")

9. ni=130;

10. nf=140;

11. for i in range(ni,nf+1):

12. dim(2)

13. row(i)

14. dim(1)



17. ax.setSpectralWidth(sw)

18. ax.setCalibrationOffsetPpm(off)

19. ax.setCarrierFrequency(frq)

20. ax.setNucleus(nuc)


21. NNB.renameData( child, "Row " + repr(i))

Discussion:

For more details about macro commands see the “Macro documentation/Commands reference” section

1. Into the variable “data”, we load the 2D spectrum “Lasalocid(JRES 1H/1H)”

2. All properties of the direct-dimension are stored into the variable “axis”

Lines 3, …, 6 are commands to store experimental parameters. These parameters are imported from “axis”

3. nuc = observed nucleus

4. sw = spectral width

5. off = calibration offset in ppm

6. frq = carrier frequency

7. Check the type of data

8. Extract the real part of the direct dimension

9. The variable “ni” indicates the number of the first row which will be extracted

10. The variable “nf” indicates the number of the last row which will be extracted

11. Iteration through the list of rows. In this example, the length of the list is 11 (140+1-130)

12. This signals that 2D data which will be handled

13. Extract the nth 1D row from the 2D data-set


15. 1D data are stored into the variable “child”. Itself stored in the current notebook

16. All properties of “child” are stored into the variable “ax”


Lines 16, …, 20 are commands to set experimental parameters. These parameters are imported from “ax”

17. observed nucleus = nuc

18. spectral width = sw

19. calibration offset in ppm = off

20. carrier frequency = frq

21. 1D spectra are renamed as follow: “row i” (with i=130, 131, …,140)

Result:

We click “Run” to execute these macro commands

As shown below, rows from 130 to 140 were extracted and stored in the notebook “JRES-Lasalocid”

Comment:

It’s very easy to use these command in order to extract column(s) from 2D spectra


You must just do these changes:


7. if ( get_itype_2d() >= 2 ):

8. real("F2")

9. ni=xxx;

10. nf=yyy;

13. col(i)

21. NNB.renameData( child, "Col " + repr(i))

1.6.3. Example 3: Sum-Extract Rows

In the “Example 2” we have show how to extract individually rows from a 2D spectrum. In this example we will show how to extract rows and how to add them together.

Added rows will be stored in the current notebook

As shown below, we create a folder called Example3-Sum-Extract-Rows. In this created folder we store the file called “sum-extract-rows.py” which contains macro commands. Then we create a new notebook called “Sum-Extract-Rows.nnb”

We start by importing experimental data “ser” which is stored in the folder “Example2-Extract-Rows/JRES-Lasalocid”

A 2D spectrum is obtained by using an automatic processing. Then we open the console and the “sum-extract-rows.py” file

As shown below, “File” (1) indicates where the file is stored on the computer



Commands:

1. data=NNB.loadCurrentData()

2. si2 = get_si2_2d();


4. nuc = axis.getNucleus()

5. sw = axis.getSpectralWidth()

6. off = axis.getCalibrationOffsetPpm()

7. frq = axis.getCarrierFrequency()

8. if ( get_itype_2d() >= 2 ):

9. real("F1")


10. dim(1)

11. chsize(si2)

12. zero()

13. put("data")

14. ni=1;

15. nf=256;

16. for i in range(1,257):

17. dim(2)

18. row(i)

19. dim(1)

20. adddata()

21. put("data")



24. ax.setNucleus(nuc)

25. ax.setSpectralWidth(sw)

26. ax.setCalibrationOffsetPpm(off)

27. ax.setCarrierFrequency(frq)

28. NNB.renameData( child, "TOTAL-Rows ")

Discussion:

For more details about macro commands see the “Macro documentation/Commands reference” section

1. Into the variable “data”, we load the 2D spectrum “Lasalocid(JRES 1H/1H)”

2. Into the variable “si2”, we store the value's size of the indirect-dimensionNMRnotebook documentation 107

3. All properties of the direct-dimension are stored into the variable “axis”

Lines 4, …, 7 are commands to store experimental parameters. These parameters are imported from “axis”

4. nuc = observed nucleus

5. sw = spectral width

6. off = calibration offset in ppm

7. frq = carrier frequency

8. Check the type of data

9. Extract the real part of the direct dimension

Lines 10, …, 13 are commands to create 1D data. Its size is “si2” and contains only zero values. This data will be added to the first extracted row


11. Set the size of 1D data to “si2”

12. Put the value zero (0.0)

13. Store data

14. The variable “ni” indicates the number of the first row which will be extracted

15. The variable “nf” indicates the number of the last row which will be extracted

16. Iteration through the list of rows. In this example, the length of the list is 256 (256+1-1)


18. Extract the nth 1D row from the 2D data-set


20. Add the contents of the DATA buffer to the current data-set.

The first time, data with zero values is added to the first extracted row. Then the (n+1)th extracted row and the (n+2)th are added together


21. Store data

22. 1D data are stored into the variable “child”. Itself stored in the current notebook

23. All properties of “child” are stored into the variable “ax”

Lines 24, …, 28 are commands to set experimental parameters. These parameters are imported from “ax”

24. observed nucleus = nuc

25. spectral width = sw

26. calibration offset in ppm = off

27. carrier frequency = frq

28. 1D spectrum is renamed as follow: “TOTAL-Rows”

Result:

We click “Run” to execute these macro commands

As shown below, rows from 1 to 256 were extracted and added and stored in the notebook “Sum-Extract-Rows”

Note that the 1D spectrum “Total” is identical to the extracted “mean” projection


Comment:

It’s very easy to use these command in order to extract column(s) from 2D spectra

You must just do these changes:

2. si1 = get_si1_2d();


8. if ( get_itype_2d() >= 2 ):

9. real("F2")

11. chsize(si1)

14. ni=xxx;

15. nf=yyy;

18. col(i)

28. NNB.renameData( child, "TOTAL-Columns")

1.7. Display

From the menu bar, click over the “Display” button to display the window shown below


Each sub-menu is described in detail (please see the sub-trees of the section "Display")

1.7.1. Zoom

• Click over the “Full Size” button to display the whole spectrum• Click over the “Define…” button to display these windows: (on the left:1D and

on the right: 2D)Then define the region you want to display by entering values manually

Note that the zoom can be done manually by following these steps:

(i) press the right mouse button at the start position of your desired zoom region and hold down the button

(ii) move the mouse cursor to the end position of the zoom region. As shown below, a box will be plotted (1)If you want, you can resize the box by positioning the mouse pointer over it (its color becomes red (2)). Then press the right mouse button, hold down it and move the mouse


(iii) finally, click (right, left or middle button) into the defined box

The result's zoom is shown below


After the zooming, note that the mini map view (4) seems different. Indeed, the size of the box (5) has been reduced

From the mini map view, you can either move or resize this box (5). This is also true for the 1D projections: (6) and (7)

We gave an example with a 2D spectrum but zooming in an 1D spectrum is done in the same way. Except that you can handle no things in the mini map view (the logo’s NMRnotebook software is displayed)

1.7.2. Layout

These menus allow you to design a layout with your notebook’s content

Note that before using these menus, you must click over the “Reduce” icon

Here an example with our notebook named STMAS-MQMAS-Shearing (see the “Shearing” section) where the two spectra are displayed in a horizontal layout

To display only one of them, click over the “Expand” icon . Then the “Reduce” icon will appear


1.7.3. OpenGL settings…

This menu allows you to use or not OpenGL.

From the “Display” menu, select “OpenGL settings…” to display the window shown below


2. Tool bar

The NMRnotebook tool bar is composed of ten buttons and each of them is described below

: Open an existing notebook or create a new one and import data in it

: Import new data into the notebook. Added data will be in the document summary

: Save current notebook

: Preview and define page printing. Permits also to export view to various graphical formats (jpeg, png, pdf, etc…)

: Print the current page as defined

: Execute a complete Automatic analysis (Fourier transform, peak picking, integration, etc…)

: Edit the Automatic analysis parameters such as apodisation, Ft algorithm, etc…

: Apply a manual phase correction

: Add peak(s) and display peak table listing

: Add integral (s) and display integral table listing (only available for 1D spectra)


3. Mini Map ViewThe mini map view allows you to explore your 2D spectra and data


4. NMRnotebook document summaryThe NMRnotebook document summary allows you to manage data contained in your notebook. We will give an example to illustrate this section

In the NMRnotebook, the automatic processing of the FID and SER files gives us a 1D and 2D spectra respectively. Note that, in the document summary (as shown below), each data is easily recognized by a specific symbol

• : 1D data acquisition

• : 1D NMR spectrum

• : 2D data acquisition

• : 2D NMR spectrum

Names near the icon are the summary's title and they are organized as following: LASALOCID (= parent folder name) 1 (= folder's name where data acquisition is stored = experiment number)

Recall that LASALOCID 1 and LASALOCID 2 are stored in the notebook_1 and notebook_2 respectively. If we choose File and Notebooks from the


Part (1) : summary's title

Part (2) : indicates notebook's name and where it is stored

Document summary options:

Left click with the mouse over LASALOCID 1, LASALOCID 1 (1D 1H) or LASALOCID 1 (1D 1H) to display the windows (A), (B) or (C) shown below

• Copy name to clipboard: to copy data name of the selected data into the clipboard

• Duplicate: To make an exact copy of files or data

o Duplicate 1D spectrum (C):

Only the spectrum is copied. Note that the spectrum name is truncated. It will completely appear when you left click over it and click on refresh (shown above)


o Duplicate FID file (B): The data acquisition (FID) and all its processed spectra (in this example we have only one) will be copied

o Duplicate the notebook content (A):

• Properties: (A): allows you to see the notebook properties (General, Author and File). (B) and (C): allows you to see the FID and the spectrum properties respectively (see the “Edit” section)

• Close: (A): To close the current notebook. (B) and (C): To disappear the selected data from the window display. In this case, Close is replaced by Show in the window

• Rename: (A): To rename the summary's title. Note that the notebook is still named notebook_1. (B) and (C): To rename the FID and the spectrum respectively

• Lock: Only for data acquisition (B)and spectra and (C). When data is locked, you cannot rename them or remove them from the document summary. Note that a bolt will appear near them: , , , and Lock is replaced by Unlock in the window

• Remove: To remove data (acquisition data (B) or spectra (C)) saved in the current notebook. Note that option isn’t available in the window (A): the notebook can be removed from the directory which contains it

• Export … : Acquisition data (B) or spectra (C) can be exported in NMRtec text format, in Gifa format and in Sparky format (only for 2D spectra). Gifa and Sparky are NMR software


• Audit: (B): This menu allows you to visualize the pulse program and the data acquisition parameters as shown below. These files (if they exist) are imported from the folders 1 and 2. Recall that folders are imported from Bruker data directory

(C): As shown below, this menu provides all processing parameters (FT, phase correction,…) which have been performed to your data. Note that if you right click: over “Show parent audit” the windows shown above will appear and over “Back”, the processing audit window will appear again


• Add folder: Available only for (A). This menu allows you to create folders which help you organize and sort your notebook content

• Here an example where we create a folder named REF-MANUAL in the notebook_1:

Note that the REF-MANUAL folder is added to the notebook and it does not appear in the LASALOCID folder

• Transfer to … : This menu is only available when there is more than one opened notebook. It allows you to transfer data from a notebook to an other. Below an example where the LASALOCID 1 spectrum and the REF-MANUAL folder are transferred from the notebook_1 to the notebook_2

o Before

o After:


Note that transferred files are kept in the notebook_1. You can also transfer simultaneously all the content's notebook_1

• Sort by name/type: Only for (A). The content's notebook can be sorted by name or by type. You can also this by the Drag and Drop operation

• Open in console: With the NMRnotebook software, you can process your data in several ways: automatic and/or manual processing (see the “Examples of processing” section). The last one can be done by using the Process menu (see the “Process” section) from the menu bar or by typing manual command lines in the console (as shown below). Several command lines (written in Python) are available (see the “commands” section)


5. Display OptionsLeft click into an empty area beside the spectra (1D or 2D), you can choose several display options (as shown below)

Each option is described in detail (please see the sub-trees of the section "Display Options")


5.1. Display parametersIn the “Display Options” window select “Display parameter…”. This will appear a new window which contains several parameters (as show below)

• Spectrum DisplayBy default, 1D spectrum is displayed as a lines display. It’s can be also displayed as dots or as lines connecting the dots display

By default, 2D spectrum is displayed as a contours display. It’s can be also displayed as a bitmap display

• Spectrum Data1D data: you can display the real and the imaginary part of the spectrum. By default, they are colored in black and in red respectively. If you want, you can change theses colors

2D data: you can display the positive and the negative (if exist) part of the spectrum

• AxisThis part allows you to display or not the chosen axis and to modify the axis unit (ppm, Hz or point)


• LayersWhen these boxes are unchecked, the corresponding parameter (peak, integral, …) will not appear on your spectrum

Only “Grid” is unchecked by default. When this box is checked, a grid will be displayed on spectrum (as shown below)

• Traces1D data: this will display the spectrum on the top (as shown below). Select the desired window size


Note that you can also change the size by left clicking in Trace window (the window shown below will appear)

2D data: this will display the 1D projections on the top (F2 dimension) and on the right (F1 dimension), as shown below

Some options are available (shown below) when you left click with the mouse in Trace window. Note, that if you have any 1D spectrum in your notebook document summary (1), the spectrum can be displayed as a 1D projection (just choose it (2))

5.2. Display and Isometric zoom modeOnly for 2D dataset


Color…: by default, the intensities are colored in green (max intensity) and blue (low intensity). These colors can be changed if you wish

Level tuning: This restores the display at the initial intensity level

You can display your 2D spectrum in an isometric zoom mode

5.3. Show parameters

This command displays some acquisition parameters which will be appear in a new window (as shown below)

This window is editable: by double clicking on it, the window below will appear and you can change or delete the text


5.4. Add…This menu allows you to add some useful objects (as shown below) into your spectrum

Each menu is described in detail (please see the sub-trees of the section "Add")


5.4.1. Add peak

Right click with your mouse on “Add peak” to add a peak to your spectrum.

When the mouse pointer is positioned over the added peak:

(i) label (s) will appear. By default, it’s displayed in ppm unit but you can change it to Hz unit (as show below)

(ii) hold down the right (or left or scroll) mouse button and move the mouse to put the peak where you want

(iii) if you press SUPPR on your keyboard, peak will be erased

(iv) click the left mouse button, “Peak Options” window will appear (as show below)

Note that peaks can be added by using either the icon from the toolbar or the Analysis menu “Peak picking” (see section “1.4.1”)

5.4.2. Add integral

This option is only available for 1D spectra and it computes integral positions

You can also add integral by using either the icon from the toolbar or the Analysis menu “Integration” (see section “1.4.2”)


5.4.3. Add note

After clicking on “Add Note”, you will see the window “Annotation options” (1) which allows you to write notes (as shown below)

When the mouse pointer is positioned over the note and if you

(i) press SUPPR on your keyboard, note will be erased

(ii) click the left mouse button, options window (2) will appear (as show below)

5.4.4. Add distance

This is useful to measure distance between two peaks (as shown below). The distance can be given in ppm, Hz or points units (1)

Position the mouse pointer over the arrow (2) (left or right), press the right mouse button and move the mouse to modify the length

When the mouse pointer is positioned over the line and if you

(i) press SUPPR on your keyboard, distance will be erased

(ii) click the left mouse button, options window (3) will appear (as show below). By default, the distance is created by horizontal orientation. Click “Shift Orientation” (3) to obtain a vertical disatance (4)


5.4.5. Add line / Add rectangle

These options are only available for a 2D spectrum. They can be used to illustrate your data

Added lines (1) are handled as added distances (please see the section "Add distance"). Moreover you can add note (2) to your added line by positioning the mouse pointer near the line (either on the right or on the left) and double clicking to write a note (please see the section "Add note").

When the mouse pointer is positioned over the rectangle corners (as shown above (5)), press the right mouse button and move the mouse to modify the size rectangle


5.4.6. Add J-coupling

This option is only available for 1D spectra and it provides a J-coupling analysis

See section “1.4.9” for more details

5.4.7. Add image

This allows you to add an image to your spectrum (either 1D or 2D) by following these steps:

(i) In “Display Options” window, click on “Add image”. Then, this icon will appear (as shown below)


(ii) Add the image, from the folder containing it, to your notebook: select File / Add data … from the menu bar or press from the toolbar. Here an example where we add the nmrtec image to the lasalocide 102 notebook. The added image will appear in the notebook document summary (as shown below)

(iii) Left click with your mouse over the icon . A window will appear (as shown below on the left). Position the mouse pointer over “Images” to see the available


image. Note that if no image is added to the notebook, the window which will be displayed is shown below (as shown below)

(iv) Right click with your mouse onto the (a) nmrtec.PNG (see above) to display the image. The result is shown below

5.5. Cursor / Correlated cursorRight click with your mouse on “Cursor” or “Correlated cursor” to display a cursor on your spectrum


The cursor (red line) indicates the chemical shift and the intensity (as shown below)

Just move the mouse (without clicking) to move the cursor


5.6. Select 1D hereThis option is only available for a 2D data

In the “Display Options” window (shown above) when you right click on “select 1D here”, two dotted lines will appear on the spectrum (as shown below).

To explore your spectrum, follow these steps:

(i) position the mouse pointer over the intersection of the two lines or over one of them. The line's color changes from black to red

(ii) hold down the right (or left or scroll) mouse button and move the mouse

or follow these steps:

(i) position the mouse pointer over Row: 186 or Col:374 (shown below). Note that the color changes and this appears: or

(ii) use the scroll mouse

When the lines are positioned over a peak(s), the corresponding 1D projections (in this example, row: 186 and Col:374) are displayed in the Traces section


5.7. Superimpose This menu allows to superimpose spectra (obtained from different experiments or processing) and to compare them

We give an example where three spectra are compared. In the document summary (as shown below) : Spectrum 1 is the original one (without any apodisation). Spectrum 2 and 3 are obtained from Spectrum 1 with 5Hz and 10 Hz exponential broadening apodisation (see the “Manual Apodisation” section)

In “Display Options” window, position the mouse pointer over “Superimpose”. Then, this window (shown below on the left) will appear. Note that if you have only one spectrum in your notebook, the superimpose button is inactive (as shown below on the right)


To superimpose spectra, you can:

(i) select the Spectrum 3 and/or Spectrum 2 check boxes (shown above)

(ii) click on “Add all”. Then, all available spectra are superimposed

(iii) click on “List …”. The window shown below will appear, then select the desired spectrum which will be superimposed

Superimposed spectra will be displayed in the window (as shown below).

Zoomed region is chosen for this example. Note that Spectrum 1 is the support and the others are added in the window display


Intensity spectra can be changed by using the scroll mouse

All intensities change when the mouse pointer is positioned over either or (or simply in the window display)

You can also change selectively the intensity when the mouse pointer is positioned over either or of the desired spectrum (the blue one for example)

Spectrum can be moved along the Y-axis with the mouse when the mouse pointer is positioned over . Or simply by using the red arrow (shown above). In this case, spectra (spectrum 2, 3) are moved simultaneously along both directions (X-axis and Y-axis)

Note that if you double click with the right mouse button over spectrum 3 (1D 1H) for example, then spectra 1 and 3 have the same position (as shown below)

You can also change the color of the spectrum by clicking on


Some options (shown below) are available when you left click with the mouse on spectrum 3 (1D 1H) for example

5.8.View full dataset, Reset and Copy to clipboardThese commands are available in the “Display Options” menu

• If zoom region (see the “zoom” section) is displayed, click on View full dataset to display the entire dataset (note that the intensity is kept unchanged). This can be also obtained by double clicking with the right mouse button in the display window or by using this button

• To reset the display (intensity and full view) click on Reset. Note that you can also use these buttons : and

• The objects contained in the display window are copied onto a clipboard when you click on Copy to clipboard. Then you can paste them in MS Word or MS PowerPoint for example


6. Display control Buttons

The usefulness of these buttons is to reset the display data (intensity and full view). It’s easily to recognize the utility of each one:

• when a zoom has been done, the left button displays the whole spectrum (1D/2D) or all of the experimental data. This can be also obtained by double clicking with the right mouse button in the display window. Note that the intensity is unchanged

• the right button resets the intensity of the spectrum or the experimental data


Documents

NMRnotebook Documentation - Software1. Drag the horizontal axis to move the spectrum in both directions. Double click to reset the zoom window 2. Drag the vertical axis to move the