Computer and chemistry: Facilitating the learning process of the infrared spectra of water and carbon dioxide
10.3280/exioa2-2023oa16829
A computational laboratory is proposed for secondary school students to facilitate the learning process of the Infrared (IR) spectra of water and carbon dioxide. In the context of the greenhouse effect, which is the macroscopic phenomenon related to the rate of cooling of our planet in response of being warmed by the sun, students can learn its molecular origin with the support of computer through the simulation of the vibrational spectra of water and carbon dioxide. Input files as well as data are provided so that the laboratory can be proposed even when computational facilities are not available. In particular, the role of computer in chemistry teaching and learning is established because molecular models let the students visualize the subnanometric world which remains elusive in daily experience.
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Laura Orian
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Computer and chemistry: Facilitating the learning process of the infrared spectra of water and carbon dioxide
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Esperienze e pratiche
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2023-11-22
2023-12-13
2024-02-21
EXIOA
Laura Orian
2023/12/13
10.3280/exioa2-2023oa16829
Università degli Studi di Padova
2499-507X
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Water
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Computer and chemistry: Facilitating the learning process of the infrared spectra of water and carbon dioxide
https://journals.francoangeli.it/index.php/exioa/article/download/16829/2580
8
Esperienze e pratiche

Computer and chemistry: Facilitating the learning
process of the infrared spectra of water and carbon
dioxide
Marco Bortoli*, Laura Orian^


Abstract
A computational laboratory is proposed for secondary school students to facilitate
the learning process of the Infrared (IR) spectra of water and carbon dioxide. In the
context of the greenhouse effect, which is the macroscopic phenomenon related to
the rate of cooling of our planet in response of being warmed by the sun, students
can learn its molecular origin with the support of computer through the simulation
of the vibrational spectra of water and carbon dioxide. Input files as well as data
are provided so that the laboratory can be proposed even when computational
facilities are not available. In particular, the role of computer in chemistry teaching
and learning is established because molecular models let the students visualize the
subnanometric world which remains elusive in daily experience.
Keywords: carbon dioxide, computational activity, greenhouse effect, infrared,
Johnstone’s triangle, water.

First submission: 28/09/2023; accepted: 08/11/2023
Available online: 13/12/2023


Introduction

   ‘Chemistry is difficult’ is the frequent complaint of students. ‘It’s hard to
teach chemistry’ is commonly reported by chemistry teachers at all levels.

*
  Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences,
University of Oslo, 0315 Oslo, Norway.
^
  Dipartimento di Scienze Chimiche Università degli Studi di Padova Via Marzolo 1
35131 Padova Italy
Il contributo è frutto di un lavoro condiviso in ogni sua parte.
Ringraziamenti.

Excellence and Innovation in Learning and Teaching (ISSNe 2499-507X), 2023, 2

Doi: 10.3280/exioa2-2023oa16829
    Johnstone (Reid, 2019, 2021) has well contextualized the difficulties in
learning chemistry by observing that chemists can see things at three levels.
Matter can be described in terms of its properties and behavior, which are
observed with the senses. This is the approach children learn in their early
childhood. But chemistry has a peculiar symbolic language which is used to
describe these observations and this coding is part of chemistry educational
programs. Finally, chemists draw explanations for the observed phenomena
using atoms and molecules, which are not visible, because they belong to the
subnanometric world. The invisible structure and organization of matter makes
understanding a challenging effort. These three aspects of chemical knowledge
are connected like the corners of a triangle (Jonhstone’s triangle), but it is not
trivial to establish such links and, in particular, the rationalization of
phenomena through particle-level interpretation creates a true cognitive barrier
for the students and represents perhaps the major challenge in chemistry
learning (Johnstone, 2010).

Figure 1 - (a) Liquid water; (b) Chemical formula of water; (c) Snapshot from a Molecular
Dynamics simulation of a sample of liquid water




    In Figure 1, the case of water is shown: on the left, liquid water can be seen;
in the middle, the chemical formula of water is written, which encodes in a
universal language the message that water is a chemical substance characterized
by identical composition independently from the different samples in which it
is present, i.e., a drink, swamp mud or sweat. Finally, on the right, a snapshot
of an atomistic simulation of water is shown, from which macroscopic physico-
chemical properties of water can be inferred such as its liquid state at room
temperature and pressure, its density, and its boiling point.
    Also, for this simple and universally known example, it is not
straightforward to link the three descriptions. In particular, Figure 1 (a) and 1
(c) show water at a different length scale, and the macro-sub nano transition is
performed using computer modeling. Nowadays there are experiments that
allow to ‘see’ atoms and molecules, thus providing a proof of concept to the
particle nature of matter, but computer simulations have proved to be faithful


                                            102
and reliable tools to represent the features of the sub nanometric world. Yet,
one should not forget that they are based on mathematical and physical
equations and rely also on a well-defined coding. While the former can be
almost ignored, at least at school level, the latter aspect deserves some attention
because it can generate confusion and misconception, In Fig. 1 (c), each water
molecule is formed by three spheres representing the three constituent atoms
i.e., two hydrogens and one oxygen, connected by two identical segments
representing the chemical bonds between each hydrogen and oxygen, The non-
linear structure and the connectivity H-O-H (rather than H-H-O as erroneously
suggested by the chemical formula H2O) stem from complex physical concepts
(quantum mechanics) or, alternatively, from an elegant chemical formalism
(Lewis formulas, Figure 1 (b)) which allows to write chemical structures
identifying the position and connectivity of atoms in a molecule without solving
the electronic problem using quantum mechanical equations. In addition, the
ball and stick representation and the color itself of the atoms are potential
sources of misconception because they may erroneously suggest that atoms are
colored spheres, bonds are rigid sticks, hydrogen is white and oxygen is red,
and so on. Thus, the simulation allows to see the sub nanometric structure of
water in a snapshot in analogous way to observing the fluid at macroscopic
level, but the students must be aware of the representation code employed.
    The example of water is a very simple case and is useful in the context of
this work. In addition, it encompasses the great potential as well as the relevant
issues related to the use of the computer in learning chemistry. Indeed, teachers
can use the computer and technology in the class to stimulate curiosity and
approach difficult concepts of chemistry at all three levels of Johnstone’s
triangle and this is the topic of the present work, which illustrates an example
focused on the molecular vibrations of water and carbon dioxide through which
they can take advantage of the computer in the class. This activity has been
proposed on several occasions in the past years by the authors in very different
circumstances, both to students from the secondary school and to chemistry
undergraduates attending computational chemistry courses, after basic courses
of physical chemistry. The level of detail was of course modulated on the level
of knowledge of the students, but the approach is identical and includes the
observation of the phenomenon, its representation, and its correct explanation;
notably, not all three levels of Johnstone’s triangle are necessarily introduced
in the computational laboratory, depending on the age and chemistry
background of the students, but are here discussed for completeness. Very
recently, an accurate similar laboratory for undergraduates, including
experimental and computational tasks, has been proposed by Hall and co-
workers (Hall & Gunning, 2023).



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   In this work, we will describe the computational activities as they can be
proposed to secondary school students, who are less familiar with radiations
and have no knowledge of quantum mechanics, providing all necessary data
and advice to run the simulations also when not all computational facilities are
available.


Discussion

    The computational laboratory is intended for secondary school students
(aged 16-18). It takes approximately four hours and should be organized in a
computing room (or online). Students can work in small groups of 2-3 people.
Ideally the teacher should introduce the topic of greenhouse effect, better if
using open questions or brainstorming, or showing a video, or even involving
the students in the construction of a small green house (one hour). In addition,
due to its importance in modern society, global warming and its short and long-
term consequences are a central topic of many scientific and political
discussions and should be included in the introductory presentation. Quite
often, global warming and the greenhouse effect are erroneously considered to
be the same. On the contrary, the greenhouse effect is a natural phenomenon,
which has allowed life on earth, whereas global warming is an effect caused by
human emissions of greenhouse gases. Moreover, the greenhouse effect is
explained to kids as well as to young learners who remain most of the times
unaware of the physical chemistry behind it. Furthermore, quite often, it is
related exclusively to carbon dioxide and/or to minor greenhouse gases,
neglecting that the most important greenhouse gas is water vapor. The
greenhouse effect is summarized in Figure 2 showing the sun radiation which
passes through the atmosphere and warms the oceans and the lands, which in
turn radiate infrared (IR) energy (heat) back to the atmosphere. Some gases can
trap this energy, which remains inside the atmosphere. If the concentration of
these gases in the atmosphere increases, more IR energy is trapped by the
atmosphere, and this causes the global warming effect.
    A second hour should be dedicated to the physical-chemical description
using the symbolic language of chemistry. Focusing on water and carbon
dioxide, the teacher should recall their chemical formulas and structure,
introduce their three-dimensional geometry with molecular models, investigate
the possible deformations from the equilibrium structure and their
representations, review the electromagnetic spectrum and in particular the
infrared region and the thermal effects of the infrared radiation. All these
concepts are found in the school textbooks. It’s the ability of the teacher to


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summarize them or to organize a more active lesson based for example on
flipped classroom.

Figure 2 - The greenhouse effect




    Finally, in the last two hours the students work in the computing room and
through the guided protocol, which will be illustrated in this paper, visualize,
interpret, and understand the molecular structure and vibrations of water and
carbon dioxide molecules, from which the greenhouse effect originates.

Approaching chemical problems at macroscopic level

     The teacher can introduce the topic by showing some images or videos or
by proposing a brainstorming, aiming at defining what a greenhouse is and why
it is used to cultivate crops and plants. Numerous examples can be found on the
Web, but these are mostly videos which include ‘the whole story’ of the
greenhouse effect, with an explanation adapted to the target public. The
observation may efficiently be limited to the phenomenon which can be
reproduced in a greenhouse, enforcing the concept that the greenhouse effect is
natural and focusing on water vapor and carbon dioxide. When presenting the
activity, the brainstorming approach seems suitable to let students share their
thoughts and misconceptions emerge. The teacher can also involve the students
in building a small greenhouse with jars or plastic bags, to let them reproduce
the warming effect (“Modelling the greenhouse effect”). In Table 1, examples
of general questions about the macroscopic problem are listed with their
connection to scientific evidence and knowledge required to interpret properly
the phenomenon.




                                       105
Table 1 - General questions to start the introductory discussion
What is a greenhouse?        In a greenhouse, the temperature is higher and favors plants’
                             lifecycle.
The electromagnetic          The sun light is an electromagnetic radiation. Bodies with
spectrum                     higher temperature emit radiations with higher energy.
Infrared radiation and       Infrared radiation can be used to transfer energy in the form of
heat                         heat
What is the role of          The atmosphere is like the glass of the greenhouse. It contains
atmosphere?                  gases (including water vapor and carbon dioxide) which let the
                             sun (body at higher temperature) radiation reach the planet, but
                             trap (absorb) the IR radiation (heat) emitted by the earth.

   Within this description, the greenhouse effect is apparently not related to
molecular aspects and, although correct, the scientific knowledge remains a bit
vague. The computational laboratory experience we have set up aims at
explaining HOW the greenhouse effect results in trapping infrared radiation
emitted from our planet and trapped by some gases in the atmosphere, focusing
on water vapor and carbon dioxide.

Approaching the symbolic language of chemistry

    When describing matter at molecular level, chemists use formulas i.e., a
symbolic language which encodes different information. In basic chemistry
courses, both at school and at the university, students learn to handwrite and
sketch different chemical formulas of different complexity. In Figure 3,
different chemical formulas of water and carbon dioxide are shown. Molecular
formulas show the actual number of atoms within each molecule, while
structural formulas represent how atoms are connected in the molecule. The
strongest limitation is that the three-dimensional aspect of the molecules is lost.
The computer is thus a valuable tool to visualize molecules as 3D objects and
this aspect of this laboratory may inspire other activities, i.e., facilitate the 3D
representation of molecules. Anyway, although 3D molecular representation is
not the focus, it is important to stress that ball-and-stick models are not exactly
a snapshot of the molecule, i.e., they are models which can be accurate and
useful, but are representations of the real molecules. Thus, students must be
aware of the information coding they are using, like atom colors, which are
assigned based on Hofmann’s croquet ball models (1865) and currently
employed in the Corey-Pauling-Koltun (CPK) notation (Corey & Pauling,
1952; Koltun, 1965), stick representation of bonds, ball size, stick length and
overall molecular shape which are rigid while real molecules at room
temperature vibrate. Despite their simplicity, we can describe water and carbon
dioxide and the procedure leading from their molecular formula to their 3D
structure.

                                                106
Figure 3 - Molecular formula (a), structural formula (b), and ball-and-stick representation of
water and carbon dioxide

           H2O

           CO2

             (a)                             (b)                                (c)

    H2O and CO2 are the chemical formulas of water and carbon dioxide,
respectively. Knowledge of the fundamentals of chemical bonding and Lewis
theory, which is explained also in the textbooks of the secondary school, is
mandatory to move from the molecular formula to the structural formula. Lewis
representation gives reason also of the bent structure of water and the linear
structure of carbon dioxide, respectively. Finally, the 3D structure can be built
using the computer. The students can use the molecular editor Avogadro
(Hanwell et al., 2012, 2023), which is a free software available for all platforms,
and draw with the mouse each molecule in separated sessions. It is not
important that the molecule is drawn with precision: Avogadro allows the pre-
optimization of molecular structures, i.e., the automated modification of bond
lengths, angles and dihedrals leading to the most stable structure.
    Then, the molecular structure can be determined with increased accuracy by
running a geometry optimization using quantum chemistry methods (DFT). For
students at the secondary school, these methods can be used as a black box,
because the formalism of quantum mechanics is beyond the curricula of their
studies.

Approaching the sub-nanometric nature of matter

   The third corner of Johnstone’s triangle regards the sub-nanometric nature
of matter i.e., its composition of atoms and molecules. This is the area in which
the use of the computer can have the strongest impact as it allows to visualize
3D structures of atoms and molecules that compose matter. This experience
aims at teaching students how to understand the role of water and carbon
dioxide in the greenhouse effect through the analysis of their calculated IR
absorption spectra.
   Introductory notions on light and matter should be qualitatively explained
based on the level of knowledge of the participants (Table 2). In particular, the
students must understand that IR absorption is associated to energy transfer as
heat and involves the interaction of light with matter. It causes rotations of the
molecules of a sample and vibrations i.e., deformation of their structure, and is

                                               107
thus strictly related to the chemical nature of the sample. This interaction with
the IR radiation explains the spectroscopic signals and the greenhouse effect as
well. In fact, the greenhouse gases like water and carbon dioxide absorb the IR
radiation emitted form the earth and the oceans and in turn re-emit it so that
heat remains trapped in the atmosphere. The accumulation of heat causes the
well-known warming, a phenomenon which has allowed the development of
life on earth and still makes it possible but can lead to excessive raise of the
temperature if the amount of greenhouse gases increases in an uncontrolled
way. Thus, the resonance frequencies (vibrational energy) of the greenhouse
gases fall in the IR energy range. At molecular level, not all vibrations are
excited by (absorb) the IR radiation, but only those which are accompanied by
a change of the molecular dipole moment. Therefore, elements of molecular
symmetry showing the most common types of normal modes (symmetric and
asymmetric stretching and bending, Figure 4) should be presented and their
effect on the molecular dipole moment clarified.

Table 2 - Basic notions needed to understand the proposed activity.
 Topic                    Explanation
                          Molecules are not fixed in space but move around by translating,
 Molecular motion         rotating and vibrating. Each of these motions mode is made up of
                          discrete (quantized) levels that can be visited by the molecule.
                          A different set of coordinates. Each coordinate, instead of
 Normal Modes             describing the position of an atom, describes a motion mode i.e., a
                          particular translation, rotation, or vibration.
                          The vectorial sum of all bonds’ dipole moments. Bond dipole
 Molecular dipole
                          moments can be defined recalling the electronegativity of the
 moment
                          different atoms.
                          IR absorption involves energies that target molecular vibrations. It
 IR absorption            is detected only if the targeted vibration involves a change in the
                          molecular dipole moment. It can be measured or calculated.

    A full step-by-step procedure of the computational lab activity is reported
in the Supporting information with all the inputs and outputs necessary. First,
the free software Avogadro can be employed to draw and pre-optimize the
molecules of water and carbon dioxide. If the computational software Gaussian
(Frisch et al., 2016) is available, the students can carry out the calculations of
the spectra inserting the coordinates obtained from the pre-optimization in the
provided input templates (see Supporting Information) and calculate the IR
spectra. In case computational facilities are not available, we have provided the
results of the calculations (see Supporting Information). The obtained outputs
can be visualized with the software ChemCraft (Andrienko, 2023) that shows
the calculated molecular vibrations and the obtained IR spectrum. Each group
can then analyze the different vibrational modes obtained from the calculation


                                                108
(Figure 4). Table 3 shows an example datasheet that can be used to collect the
results. The teacher can then proceed to discuss the results of one of the two
compounds. Additional details on the physical properties of the vibrations can
be highlighted and confirmed by the numbers obtained e.g., the fact that
bendings are found at lower energies than stretchings or that normal modes that
are equivalent by symmetry have the same energy. The second compound
should be left as a test for the students to do on their own.

Figure 4 - Vibrational modes of water. In the stretching vibrational mode, the OH bond lengths
can change in a symmetric fashion (a) or asymmetrically (b); the bending vibrational mode
affects the HOH angle amplitude (c)




              (a)                             (b)                             (c)

Table 3 - Example datasheet for the analysis of the calculated results
     Compound
 Vibration nr.     Wavenumber         Intensity      Mode type           Visible in spectrum?
 1
 2
 3
 4



Evaluation and assessment

    The evaluation of the activity is carried out by grading the report sheets (see
an example in Table 3) for both compounds for each group. One point is given
if the field is correct, none if not. A passing score of 60% of correct answers
and an excellence score of 90% were used in the test sessions for the activity.
We evaluated the activity on two classes of 21 and 24 students and in both
around 90% of the students passed, with more than half exceeding the
excellency level. The most common mistakes involved mainly the second
compound that was carried out by the students without the teacher’s guidance
and regarded the recognition of the mode type. The aggregated results should
be shared with the students to assess which were the most common errors and
try to understand why the underlying concepts were not fully understood.
    Finally, an open discussion should conclude the activity to put the
calculations into the greenhouse effect context. Students should be asked to try


                                                109
and make a connection between the calculated IR spectra and the macroscopic
greenhouse effect exerted by water and carbon dioxide. The teacher should act
as a guide to make sure that the link between the molecular properties and the
macroscopic effect they have in the greenhouse effect is clearly outlined. If
there is a good response from the class, the discussion can be furthered asking
the students to make predictions on the possibility of some of the other
substances present in the atmosphere to be or not to be (this is the case of the
abundant molecular oxygen and molecular nitrogen) greenhouse gases. Since
typically students enjoy looking at molecular vibrations, exercises can be
proposed to classify them for different molecules and predict if they are IR
active. To this purpose, at the end of the lab, the teacher can propose to install
an app on the mobile phone, MolAr (“MolAR”), which allows to visualize the
vibrational normal modes of a lot of molecules with their classification and
eventually prepare interactive exercises.


Conclusions and perspectives

    The greenhouse effect is a good example of a pressing environmental
challenge that can be used in a secondary school activity to explore all three
levels of chemistry (Reid, 2019, 2021). Our computational laboratory aims at
explaining the origin of this phenomenon through the calculation of the IR
spectra of two fundamental components of the atmosphere, water and carbon
dioxide, using a robust protocol. The procedure can directly show, using the
symbolic language of chemistry, how the macroscopic atmospheric effects are
caused by the intrinsic properties of microscopic objects.
    The use of all three levels of chemistry in the same experience is often hard
to find in secondary school curricula that usually focus on only one of the
aspects, leaving students with a series of uncorrelated pieces of knowledge that
are hard to assimilate. With the combination of calculations, that give access to
the elusive microscopic world, and the introduction of more interactive
teaching strategies actively involving students, we believe that it will be
possible to create more effective chemistry programs encompassing all the
corners of Johnstone’s triangle that will result in enhanced competence and
likely in students saying ‘Chemistry is fun!’ and teachers replying, ‘It’s a
pleasure to teach chemistry!’.


References

Andrienko, G. A. (2023). Chemcraft - graphical software for visualization of quantum

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    chemistry computations (Version Version 1.8, build 654). Retrieved from
    https://www.chemcraftprog.com.
Corey, R. B., & Pauling, L. (1952). Molecular Models of Amino Acids, Peptides, and
    Proteins. Review of Scientific Instruments, 24(8), 621-627. doi: 10.1063/1.1770803.
Frisch, M. J., Trucks, G. W., Schlegel, H. B., Scuseria, G. E., Robb, M. A., Cheeseman,
    J. R., . . . Fox, D. J. (2016). Gaussian 16 Rev. C.01. Wallingford, CT.
Hall, W. P., & Gunning, L. (2023). Physical Chemistry in Context: Using Quantum
    Mechanics to Understand the Greenhouse Effect. Journal of Chemical Education,
    100(3), 1333-1342. doi: 10.1021/acs.jchemed.2c00550.
Hanwell, M. D., Curtis, D. E., Lonie, D. C., Vandermeersch, T., Zurek, E., &
    Hutchison, G. R. (2012). Avogadro: an advanced semantic chemical editor,
    visualization, and analysis platform. Journal of Cheminformatics, 4(1), 17. doi:
    10.1186/1758-2946-4-17.
Hanwell, M. D., Curtis, D. E., Lonie, D. C., Vandermeersch, T., Zurek, E., & Hutchison, G.
    R. (2023). Avogadro2: an open-source molecular builder and visualization tool.
    (Version 1.97.0). Retrieved from https://www.openchemistry.org/projects/avogadro2/.
Johnstone, A. H. (2010). You Can’t Get There from Here. Journal of Chemical
    Education, 87(1), 22-29. doi: 10.1021/ed800026d.
Koltun, W. L. (1965). USA Patent No. US3170246A.
Modelling the greenhouse effect. Retrieved from https://edu.rsc.org/experiments/modelling-
    the-greenhouse-effect/1543.article.
MolAR. Retrieved from https://mtzgroup.github.io/molar/about/.
Reid, N. (2019). A tribute to Professor Alex H Johnstone (1930-2017) His unique
    contribution to chemistry education research. Chemistry Teacher International,
    1(1). doi: 10.1515/cti-2018-0016.
Reid, N. (2021). The Johnstone Triangle: The Key to Understanding Chemistry. The
    Royal Society of Chemistry.


Appendix

IR Spectra calculation procedure

    To calculate the IR spectrum of water or carbon dioxide the first step is to
create the 3D model of the molecule. The free software Avogadro
(https://www.openchemistry.org/projects/avogadro2/) will be used to draw the
spatial structure of the molecule and then pre-optimize the geometry with the
in-built force field engine. After launching, Avogadro presents a black window
where molecules can be drawn (Figure S1, a). Using the pencil tool atoms of
different elements can be added (Figure S1 b). As the drawn molecular structure
is usually not good, a pre-optimization is carried out that should bring the
molecule closer to its equilibrium geometry (Figure S1, c). The coordinates of



                                            111
the pre-optimized structure can be extracted and used for the DFT calculation
using Gaussian (Figure S1, d).


Figure S1 - Avogadro 2 steps to obtain the initial pre-optimized coordinates of water. Initial
Avogadro 2 screen (a); Drawing tool to insert the required atoms (b); Force field geometry
optimization menu (c), and cartesian coordinates editor (d)




     (a)




                                              112
    (c)




   The actual IR spectrum is calculated at the DFT level with Gaussian. The
template input for the calculation is the following:
   %mem=8GB
   %nprocshare=8
   %chk=opt.chk
   #p b3lyp/6-311G(d,p) opt freq

   title

   01
   O -0.032562940 0.000000000 -0.421603299
   H -0.032562940 0.759337000 0.174439701
   H -0.032562940 -0.759337000 0.174439701
   The first line is the amount of RAM requested for the calculation, the second
the number of CPUs, and the third the name of the checkpoint file that will be
created. These can be changed in relation to the available computational
resources. The line starting with #p is the so-called route and it contains all the


                                         113
parameters for the calculation. In this case the functional B3LYP and the basis
set 6-311G(d,p) are chosen. In addition, a geometry optimization (opt) and a
frequency calculation (freq) are requested. The route line is followed by a blank
space, the title line that contains the name of the calculation, and by the
molecule specification. The latter starts with a line containing the charge (0)
and the multiplicity (1 for a singlet) of the molecule and is followed by the
molecular coordinates. In this example the coordinates for a molecule of water
are reported. They can be substituted with the coordinates of the molecule for
which the IR spectrum must be calculated. IMPORTANT: the use of blank
lines in Gaussian is very precise and exactly one blank line must separate route
from title and title from molecule specification. Moreover, the input file must
always end with a blank line otherwise the calculation will not run.
    The gaussian calculations can be run by executing the g16 command on the
created input file. It will create a text file with .log extension. If the calculation
correctly ended, the last line of the .log file should read “Normal termination of
Gaussian”. In case the Gaussian software is not available we have provided the
output files as supplementary material.
    The outputs can be opened with the software ChemCraft
(https://www.chemcraftprog.com) to visualize the molecular vibrations and the
IR spectrum. ChemCraft is a paid software that offers a trial period and can
therefore be downloaded and used for free for a period of 150 days. The main
steps needed to open the Gaussian results and visualize the vibrations and IR
spectrum are reported in Figure S2.

Figure S2 - ChemCraft steps to visualize the molecular vibrations and the IR spectrum. Initial
ChemCraft screen and open file menu (a), molecular vibrations list under Frequency section in the
left-hand side of the screen (b), the spectra visualization menu available when the entry Frequencies
on the left hand side is selected (c), and the IR spectrum visualized from ChemCraft (d)




     (a)



                                                  114
(b)




(c)




      115
