“FOURIER TRANSFORM EXPLAINED” WEB APPLICATION

TEACHER’S GUIDE

A. General Notes:
This web application is intended to be a self-instruction tool. Nevertheless, some students, especially
5those with weak mathematical background, might need help from the teacher, before or (better)
after they try the app.

The application is not intended to be a complete NMR course. This is why it is important to inform
the students that subjects like chemical shifts and proton-proton coupling are not treated by the
proposed app.

10In this guide, additional experience from the feedbacks obtained from students and colleagues was
added.

B. How to run the app:

There are two ways to run the app:

1-By visiting the app web site:

15https://ftnmr.eu.pythonanywhere.com/

This option needs an internet connection. All the calculations are done on a distant server, and no
files are downloaded on the local computer. The app is adapted to desktop computers as well as
smartphones and tablets.

2-By downloading executive files (for Windows PC only):

20This option is adapted for users with no permanent internet connection. Once the app downloaded,
it doesn’t need internet connection and can be run on the local computer.

The executive files as well as the instructions to run the app are available from the authors’ website:

https://clarolineconnect.univ-lyon1.fr/icap_website/view/2018

C. Lesson plan and pedagogical objectives:

25This web application has several pedagogical aims, which can be achieved by following the steps
below. Within these steps, we included suggested answers to most frequent users’ interrogations 1:

1-Showing the constitution of an FID by adding individual proton resonances:

1
Most of these questions raised about old versions of the application and helped us improving it.

1
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This is the first step of the application. It is achieved by clicking on “Add Frequency” button. The FID is
automatically updated in graph 2 when adding new protons. The frequencies can be entered
30manually in the “Frequency” input field, otherwise the application will choose a random frequency
each time the “Add Frequency” button is clicked.

In the initial run, the frequencies are limited from 1 to 10 Hz, but this can be changed afterward in
the Parameters screen. We advise the user not to use high frequencies, which can be less visible in
the graph.

35We would like to draw the teacher’s attention to the fact that the scale of the FID graph is not the
same than that of the “One proton resonances” graph: the latter is always from -1 to 1 while the
former grows up when adding more protons.

Teaching Experience: The constitution of the FID, as a sum of individual resonances, is generally well
understood by the students. They appreciated the fact that they can observe, for the first time during
40their cursus, how an FID is updated when adding additional protons.

2-Explaining how a spectrum is generated from an FID:

This is the key point of the application. After the student added up to 4 frequencies, he/she can click
on “Fourier Transform” button. This will start a step-by-step explanation of the FT procedure. The
transition from one step to the next one is done by clicking on “Next” button, and finally the
45animation can be loaded from the server. The student can pause the animation, play it continuously
or frame-by-frame, in forward or backward direction.

Teaching Experience: This is the point that needs the more time to be understood by the student,
and depending on student’s mathematical knowledge, it can require teacher’s assistance. The
explanation messages given with the application were optimized to answer the key difficulties usually
50encountered by students and/or reported by reviewers and colleagues. Some of the most
encountered interrogations are reported hereafter:

a- “The computer knows which frequencies are present in the FID. Why is he looking for them
by doing FT?”

It is important that the student understand that the computer ignores which frequencies are
55 present in the FID. The first step of the app (i.e. adding protons to the FID) is visible only by
the student, and is not “visible” by the computer program who looks for the frequencies by
applying the FT.

b- “What are trial frequencies?”

Depending on their mathematical background, some students can need help with the notions
60 of frequency and cosine function. If this is the case, the teacher can advise the student to run
the application to the end and to see the animation by focusing only on the FID graph (graph
2). The student can observe the depiction of trial cosine functions with growing frequencies.
After this is done, the student can run the Fourier Transform once more in order to see the
rest of the procedure.

65 c- “How are FID and Trial Frequency functions multiplied?”

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 We answered this recurrent question by giving a detailed example in explanation messages
found in the app.

d- “How is the area under the curve calculated?”

Some students have memories from high school, where they used to calculate areas under a
70 function curve by finding the primitive function and then calculating the definite integral. The
teacher should explain that this is not how the computer processes in this case. The
computer does not have the equation of the (FID*Trial Frequency) function and consequently
cannot find its primitive function. Instead, the computer uses a numerical method which
breaks the area under the curve into very small trapezoids and then calculates the sum of the
75 areas of all these trapezoids.

e- “Why the area under (FID*Trial Frequency) curve is close to zero when the trial frequency
does not correspond to any hidden frequency in the FID?”

This is a recurrent question. We recognize that giving a strict mathematical demonstration of

this postulate is not the aim of the application. But we advise the teacher to use the
80 following analogy with a simple cosine function: The area under a cosine curve is always zero
(if we calculate it over an integer number of periods 1). If we multiply a cosine function by
another random function, the resulting function will also have a zero area, because it will
follow the cosine function oscillation. The only case where the resulting multiplication curve
has an area different from zero is when the FID has a hidden frequency that corresponds to
85 the cosine function (i.e. the trial frequency). This point was illustrated by an example image
in the application.

f- “What about proton-proton coupling?”

While our application is not intended to deal with coupling phenomena, the teacher can
answer this question by reminding the student that proton-proton coupling splits the proton
90 population into two or more populations with different frequencies.
Within our application, a doublet can be depicted by the FT processing of two proton
frequencies (e.g. 5 Hz and 6 Hz). A triplet can be depicted by the FT processing of 4 proton
frequencies (e.g. 4 Hz, 5 Hz, 5 Hz and 6 Hz). More complicated coupling schemes
(quadruplets, etc.) cannot be correctly represented in our application, which is limited to 4
95 frequency populations with equivalent intensity.

3-Showing the effect of some parameters on the final spectrum:

After the student has observed the animation, he/she is invited by the application to change
parameters that have an impact on the FT. He/she can then restart the FT process with the new

1
We took the example of an integer number of periods for simplification, but whether the integral is calculated
10over an integer number of periods or not, we can show mathematically that:
A
1
∫ cos ( 2 π∗freq∗x ) . dx= 2 π∗freq ∗sin ⁡(2 π∗freq∗A )
0
For large frequencies like those of NMR signals, this integral will be very close to zero whatever the value of A,
1
because the term will tend to zero while the value of the sine function is always between -1 and 1.
2 π∗freq

15 3
 parameters. An explanation message can be obtained for each parameter by clicking on the
100corresponding “?” button in the parameter screen.

Teaching experience: These are some pedagogically interesting effects that the student can observe
and link to his/her general NMR knowledge:

a- The effect of the nucleus decay constant on the spectrum peak width: This can be
demonstrated by the equation of the lorentzian peak resulting from the FT (see textbooks
105 below).
b- The effect of the acquisition time on the noise in the spectrum (after adding noise to the
FID): the origin of this effect is explained in the corresponding explanation message.
c- The effect of the signal phase on the peaks shape: It is worthy to note that the trial
frequencies used during the FT process in this application have a zero phase, and that the
110 “Signal phase” parameter is the difference between the signal phase and the trial
frequencies phase.

A lot of students’ questions may arise from this part of the application. Meanwhile, the application is
not intended to be a complete NMR course. The explanation messages for the parameters describe
the effect of these parameters on the FT process but do not explain all the mathematics and physics
115behind these phenomena.

In order to obtain more detailed answers to these questions, the teacher can recommend these
references covering the acquisition of NMR spectrum in a simplified manner (accessible to chemistry
students):

1- Keeler, J. Understanding NMR spectroscopy, 2nd ed.; Wiley: 2010.

120 Chapter 5: Fourier transformation and data processing

Chapter 13: How the spectrometer works

2- Jacobsen, N.E. NMR spectroscopy explained; Wiley: 2007.

Chapter 3: NMR Hardware and Software

3- Hornak, J.P. The basics of NMR. https://www.cis.rit.edu/htbooks/nmr/ (accessed Oct 2019)

125 Chapter 5: Fourier Transforms

D. Evaluation:
In order to evaluate our applications, a French version of the software was introduced during an
NMR course to a class of 34 students following a “Master Ingénierie de la Santé” in the faculty of
pharmacy of Lyon, France (students following a 1st year of Master’s degree in health technologies
130after a 3 year cursus in biochemistry, chemistry or biology). The application was also evaluated by
Ph.D. students and organic and analytical chemistry teachers not specialized in NMR techniques.

The feedbacks were gathered using a survey (a link to a Google Form was added to the application
during the test period). We present below the compiled answers we obtained from the survey
(N=22).

135a-Scientific background:

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1-Are you familiar with NMR spectra interpretation? Yes 86%

2-Have you ever heard about the Fourier transformation process? Yes 86%

3-Do you know how FT actually proceeds? No 95%

b-About the manner with which the software was used:

140 1-Have you encountered technical problems with the software (slow server response, etc.)?
No 100%

2-How many times have you run the application in order to understand the process? 1 time:
36% // 2 times: 55% // >2 times: 9%

3-How much time have you spent on the application? 15 minutes in average

145c-About the usefulness of the application:

1-Did you understand these points after running the application:

-The generation of the FID from individual resonances: Yes 95%

-The multiplication of the FID by trial frequencies: Yes 95%

-The generation of NMR spectrum by the FT process: Yes 86%

150 2-About the parameters:

-Did you try to change the parameters? Yes 77%

-Did you find the parameters explanation messages useful? Yes 95%

d-Free comments section:

Would you have any recommendation to the authors to improve the application?

155 Most of the recommendations were about the graphical interface of the application, which
some students did not find “colorful” enough. Also, some students suggested to make the
application more playful.