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Basic processing of 1D NMR spectra in MestReNova
This brief tutorial will introduce you to the basic operation of the MestReNova (MNova) NMR
processing software. For this example lesson, we will be working with the spectrum for ethyl
acetoacetate. Using this tutorial you will learn the following:
1. How to download and open an NMR file (a .fid file) within MNova
2. How to view portions of a spectrum, including zooming in to signals and zooming out to
view the full spectrum
3. How to “peak pick” to list a peak frequency in units of Hz or PPM.
4. How to integrate the area under a signal and change the base integral value
5. How to annotate, save, and print your processed spectrum as a PDF.
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Starting MNova
Begin by launching the MestReNova (MNova) software program (double click the desktop icon
or launch it from the “Start” menu). The software will take a few moments to load. Ignore any
license warnings or ask your TA if you are having difficulties.
1. Opening FID files
After starting MNova, you also will need to download the FID file for the example molecule ethyl
acetoacetate.
You can find the ethyl acetoacetate fid on the 347 class website by navigating your browser to
the website and clicking through Software & Web Resources > NMR Software. You will see a
link here for the ethyl acetoacetate.fid.zip file. Click on the link and it will save it automatically to
the Downloads directory on the computer.
Now you will need to open the FID file using MNova. This FID file is the file which contains the
raw data acquired during the NMR experiment.
Navigate to the File menu, select Open, and locate the FID file you
downloaded. It should be located in the Downloads directory. You can open
the zip file directly, without needing to extract it.
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After opening the FID in MNova, you should now see the full spectrum in the main window.
MestReNova has automatically applied a Fourier transform operation on the raw data to arrive
at the spectrum you are viewing.
Next, we will see how to zoom in and explore different signals within the spectrum.
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2. Exploring the NMR Spectrum
Now you can explore the various parts of the spectrum using some of the tools within MNova.
There are a number of useful tools on the top tool bar.
2.1 Zoom in
The magnifying glass with the (+) icon above it is called the “zoom in” tool, which will allow you
to select a region of the spectrum and zoom into that area. Use it by clicking the mouse button
down
and
dragging
it
across
an
area
to
zoom
in
as
shown
Click and drag the “zoom in tool” around a signal
Release the mouse button to zoom in on that area.
below:
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2.2 View full spectrum
To return to the full spectrum view, select the “Full Spectrum” button on the toolbar. This will
display the entire spectrum again, and you can then zoom in close on a different signal.
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3. Peak analysis
In order to analyze a spectrum, it is necessary to obtain several pieces of information by
examining individual signals and their associated peaks. Some of the most basic information
includes:

The chemical shift of a peak (in ppm and/or Hz)

The splitting pattern of a signal (triplet, doublet, quartet etc.)

The separation between two peaks within a split signal (in Hz)
To obtain this information within MNova, we will be using a “Peak Picking” tool called “Peak by
Peak” analysis.
Start by clicking the Peak picking tool drop down arrow as the red circle above shows, and then
select “Peak by Peak”
It is very important that you use the “Peak by Peak” tool and not the “Automatic” option,
otherwise MNova will try to figure things out on its own and make mistakes, as well as make it
more difficult to find the information you need.
Now that you have the peak picking tool selected, you can pick a particular peak and click with
the mouse button. Doing so will display the peak frequency (in units of ppm) on top of the
spectrum for you to see.
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Try this:
1. Display the full spectrum
2. Zoom in to the quartet that is between 4.15 and 4.21. You
should see something like the image on the right.
3. Now choose the “peak by peak” tool from the Peak picking
drop down as shown above and pick the four peaks along the
signal.
4. If you look at the top of the window you will now see the four
peak signals listed in ppm (4.20, 4.19, 4.18, 4.16).
It should now look something like this:
Notice also you can see the value (in ppm) along the x axis at the bottom of the spectrum. It
would be more useful now to see the values of the peaks in units of Hz, so you can calculate the
coupling constant J for this signal. We have to tell MNova to display peaks in Hz rather than
ppm.
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Displaying peaks in Hz units
If you use the right mouse button and click on the white space above in the spectrum, a small
context window will appear. Choose “properties
Right click in the whitespace of the
spectrum
Choose “Properties”
You will see a list of items for which you can change the
properties.
Select “Peaks”
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Now look on the right side of the window and find the “Units” drop down box (which will say
ppm). If you click on the drop down box you will see the option to use “Hz”:
Select Hz, and hit the “Apply” button. Finally close this window by pressing the “Ok” button.
Alright, now you should see your
peaks listed in units of Hz at the
top of the spectrum.
It will stay this way for all the
peaks you pick within the
spectrum until you exit the
program or change the units back
to ppm using the properties menu.
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Now you can view the full spectrum and use the “Peak by Peak” tool to assign Hz values for all
of your peaks within the spectrum. You will need these values in order to assign coupling
constants to the signals within the spectrum.
Once you have completed this, move on to the next section to learn how to integrate each of the
signals.
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4. Peak Integration
The area under the peaks within a signal can be determined using the integration tool within
MNova. We will be using the manual integration tool which will allow us to measure the ratios of
protons within a given signal.
Click the drop down arrow next to the integration tool button and select “Manual”
You can now click and drag an area around a signal and an integral will be calculated for that
signal.
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You will now see a new integral curve above your signal and the normalized integral value
below the signal.
It is important to note that
THE FIRST INTEGRAL YOU DRAW WILL AUTOMATICALLY ASSIGNED THE VALUE 1.
All subsequent integrals you draw will be some factor of this first integral. You will learn how to
change this default value in the next step. Continue by integrating each of the signals in your
spectrum. When you are done, you should see something like this:
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The values for your integrals might be slightly different, which is fine. Now suppose you know
that the integral for the quartet at ~4.2 ppm not actually 1.00, but in fact more like 2.00. This is
easy to change.
You can edit the value for any single integral you wish and the software will automatically adjust
all the remaining integrals accordingly (their ratios were determined when you drew the actual
integration curve). All of this is done using the “integral manager”.
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How to access the integral manager:

Select the manual integration tool as before

Move the cursor over the integral “span line” below the signal until it is illuminated as
shown

Double click the mouse button

You can also just double click the integral curve symbol above the peak signals as well
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This is the integral manager dialog box. Here you can adjust the normalized value of the
selected integral by typing in a new value (such as 2.00) and pressing the “Enter” button. When
you do that, it will adjust this integral, and all the other integrals in the spectrum.
You can use the left and right blue arrow buttons at the top of this window to navigate through
your integrals. Do not adjust any of the other values or press the various buttons, as it will
change your integrals to values you do not expect.
Next you will learn how to save your processed spectrum and export it as a PDF file for your lab
notebook records.
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5. Annotating, saving, and exporting your work.
You can save the processed MNova file by using the file menu and choosing “save as”, just as
you normally would in any other software program. The file format is a .mnova file, and it will
contain all of the formatting and processing you have performed on the file. You can email
yourself this file, save it to a cloud file service/dropbox, etc.
To annotate (make notes) on your spectrum, such as the spectrometer frequency, your name,
the experiment number, or signal assignment notes you can use the “text” tool. Find this tool
down in the lower left hand corner of the screen where the “arrow” is located and click the drop
down menu. Select “Text”.
You can use this to enter text anywhere on the spectrum document. Font size and color options
are right along the bottom portion of the window.
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Exporting as a PDF
Before you exit, you should also make sure to save the file as a PDF which will print nicely and
can be viewed on any computer without the need for MNova.
First, use the zoom in tool to expand the region that you want visible in the PDF file.
When you are happy with the appearance of the spectrum choose “Export to PDF”
Type in a file name and click save. You now will find a PDF of your processed spectrum which
you should save to a permanent location for the class and also print a copy for yourself to have
in your lab notebook.