1. health and fitness
2. disease
3. cholesterol

Chem. Educator 2009, 14, 1–4
(web)1
Why Do Students have to Learn about Molecular Structure and Chemical
Bonding?
Maria Vlassi* and Alexandra Lymperopoulou-Karaliota
Department of Chemistry, University of Athens, Panepistimioupolis Zografou 15771, Athens-Greece,
[email protected]
Received July 30, 2008. Accepted July 1 2009
Abstract: The fact that the objects have many differences in their properties is due to the structure of the
compounds as well as the kinds of chemical bonding. The main goal of this study is to suggest some interested
examples and applications from the students’ everyday life combined with the structure and bonding. These
examples are introduced through a scenario of an undergraduate student’s daily routine. The answers of the
student’s queries posed in the scenario indicate why students have to learn about molecular structure and
chemical bonding.
Introduction
The chemical structure and the bonding are central concepts
in the chemistry teaching, which are essential for
understanding of almost every other topic in chemistry such as
carbon compounds, proteins, polymers, acids and bases,
chemical energy and thermodynamics [1]. The fact that the
objects have many differences in their properties is caused not
only by the structure of the compounds but also by the types of
chemical bonds that are developed when the atoms or the ions
are connected with each other (intramolecular bonding) as well
as the way in which the molecules interact with each other
(intermolecular bonding).
According to Linus Pauling “beginning courses in chemistry
should emphasize the simpler aspects of molecular structure in
relation to the properties of substances. These aspects include
the electronic structures of atoms, with emphasis on the noble
gas structure, the shared electron-pair bond, the tetrahedral
carbon atom, the electronegativity scale, partial ionic character
of bonds and the idea of resonance as applied to the benzene
molecule” [2].
The importance of the molecular structure is confirmed by
an old as well as a modern philosopher through their
statements. When Descartes, the older philosopher, was in
Amsterdam, he kept observing the snow for two continuous
days. Within the exceptional description of the snowflakes he
predicted the ice structure: “…What surprised me the most was
the fact that among the falling snowflakes there were some
with 6 small teeth around them like the toothed wheels of a
clock. The next morning, there were small ice plates, so flat, so
shiny, so transparent and in such perfect hexagons, that a
human hand couldn’t have made them with such precision”
[3]. Also, Roald Hoffmann, in one of his lectures, wanting to
associate scientific knowledge with everyday applications and
to emphasize the importance of the structure of chemical
substances used the hemoglobin molecule as an example. He
quoted that “watching its structure is like watching a mass of
tangled spaghetti or a worm nest. So where is the beauty in
such a molecule? Why is the knowledge of such a structure
important? The answer lies within the result that this structure
brings: hemoglobin is necessary for the transportation of
oxygen in blood, which is an essential process for the function
of the human organism” [4].
In order to identify whether Greek students can combined
the properties of some substances or compounds they use in
their every day life with the molecular structure and the kinds
of chemical bonding, we proceeded to a research with 142
participated students who had just entered the university with
excellent marks in chemistry entrance examination. Another
goal of this previous study was to investigate students’
misconceptions about chemical bonding in relation to the
teaching methods and the curriculum. The results demonstrated
that students have difficulty in connecting the microcosm with
the macrocosm and in realizing the relation between the
properties of a chemical compound or a material and the types
of chemical bonding that appear in it. Also, many
misconceptions about the chemical bonding were observed [5].
These misapprehensions will continue existing unless the
golden rule of educational practice is applied. As Ausubel
stated, “teaching should be done according to what students
already know” [6].
Several techniques and methods that used and introduced
real-world examples in the classroom in order to illustrate the
relevance of chemistry to students’ everyday lives have been
reported [7–11]. In one of those reported papers titled “Why
Do I Have to Study Chemistry?” Barker presented a long list
of questions posed by a student through his or her daily routine
to prepare to go to class. Each question of the scenario can be
answered by the knowledge that would be gained in the
chemistry class [12].
The previous investigation as well as the Barker’s article
was the cause for preparing the present work. Except from
indicating the necessity of learning about the chemical bonding
and the chemical structure, another basic aim is to suggest
some interested examples and applications from the students’
everyday life combined with the structure and bonding. These
applications are introduced through a scenario of Jason’s daily
routine. Jason, the hero of the study, is an undergraduate
student that during the day wonders about various phenomena
and properties of the substances he meets around him. Some of
these queries (many naïve ones) can be explained in the
chemistry course through the teaching of the molecular
© 2009 The Chemical Educator, S1430-4171(09)0xxxx-x, Published on Web 12/29/2009, 10.1333/s00897092221a, xxxxxxaa.pdf
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Chem. Educator, Vol. 14, No. X, 2009
structure and chemical bonding. One possible activity can be a
writing-in-chemistry assignment in which students answer the
questions posed in the scenario. If the undergraduate students
are assigned the writing-in-chemistry activity, it is likely that
they will need access to a library with fairly extensive
references in chemistry. Although the answers to the questions
are given into this paper, this scenario can be shared to the
students as a project without the explanations. Two of the
applications that refer to the interesting subject of nutrition (cis
– trans isomers of fatty acids and the Greek drink called ouzo)
are widely discussed.
Scenario. The day begins and Jason is preparing for the
college. As he finishes showering he dries himself with a
towel. He looks at the label, which indicates 100% cotton and
he thinks: “How does my body dries with the cotton towel?”
From the chemistry and biology course it is known that
cellulose is a linear polymer which consists of glucose
molecules linked by glycosidic bonds and includes hydroxyl (ΟΗ) reactive groups. This is why it is also characterized as a
polysaccharide. While we use the towel the water is removed
from our body through the gaps of the cellulose fibers.
Additionally the water forms strong hydrogen bonds with
cellulose. These hydrogen bonds are stronger than the
intermolecular forces between the water and our body.
Therefore, the water molecules leave our body and so it dries
[13].
On the way to the college Jason stops to fill the car with
gasoline. He thinks: “Which type of gasoline is considered to
be of finest quality; 95-octane or 100-octane gasoline?” Later,
his chemistry teacher gives the explanation. The gasoline
enters the internal combustion engine’s cylinders with air. The
fuel–air mixture is pressurized inside the cylinders where it is
ignited by spark plugs. However, when the pressure exceeds a
certain value, which depends on the fuel’s quality, the ignition
does not take place normally but on the contrary the fuel
autoignition is produced. Then a characteristic sound is heard,
which is called “knocking” and is created by the effect of the
impact wave of the fuel’s pre-ignition to the engine cylinder
wall. The higher this temperature is the greater is the antiknocking ability of the gasoline, which means that the longer it
can resist to an increased pressure without knocking. The
students know that gasoline is a mixture of hydrocarbons with
5 to 12 carbon atoms. The more highly branched the
hydrocarbon molecules are, the weaker the London forces
developed between these molecules will be and the degree of
packing is lower than in the less branched molecules. The
molecules that are harder to pack (i.e. the highly branched
ones) are the ones that resist high pressure. The process during
which the molecules become more branched is called gasoline
reforming [14].
The lesson starts. As he is writing, he wonders “how does
the pencil write on the paper?”
The explanation is that graphite is a crystal form of carbon.
The graphite crystal consists of flat layers of carbon atoms,
which are connected to each other by forming regular
hexagons [15]. This makes graphite soft. Intermolecular forces
between the graphite and the paper cellulose are stronger than
the cohesive forces that appear among the carbon atoms in
graphite. Thus, graphite remains above paper.
The bell rings for the break. As Jason gets up from his chair
he realizes that there is a chewing gum stuck to his trousers.
This is obviously a practical joke. Angry, he shouts: “Now
how will I get the gum off my trousers?” Thanks to his good
Vlassi et al.
luck the chemistry teacher gives him the solution. The basic
ingredient of the commercial traded chewing gum is polyvinyl
acetate (PVA), a polymer which belongs to the category of
elastomers and provides the chewing gum with its elastic and
adhesive properties. Weak intermolecular covalent Van der
Waals forces develop among the linear chains of this polymer
and also explain the elastic properties of the gum. In order to
remove the gum from his trousers, Jason must place some ice
cubes (in a nylon bag) on the gum, in order to freeze it [16].
The temperature decrease results in strengthening the
intermolecular forces and bringing the polymer molecules
closer, so that the gum becomes very hard. In this way, the
cohesive forces between the molecules of the textile fibers and
the gum become weaker than the relative forces among the
gum polymer molecules and therefore the gum can be easily
broken like a glass and removed from the fabric.
The lesson ends. Jason gives in to temptation and buys
potato chips from the college coffee bar. He reads the label at
the back of the package and wonders: “These potato chips
contain 34 g of fat. Only 16 of them are saturated which are
said to be unhealthy. The rest are unsaturated. Is this
unsaturated fat beneficial?” Next day, in chemistry course, the
answer will be given to him. Trans-unsaturated fatty acids are
produced from their cis isomers during partial hydrogenation
procedures used by the food industry to harden oils. Transfatty acids are consequently found in a variety of food products
[17]. During processing of the oils or their partial
hydrogenation, some double bonds are converted to the more
stable trans configuration [18]. Industrially produced transfatty acids have received some attention lately due to their
potentially hazardous health effects. The fatty acid
composition of potato chips is affected by the oil used for
frying. The chips are high in cis and trans oleic acids and also
contain palmitic, and linoleic acid in a lower percent. [19] The
presence of cis double bonds requires a change of the chain
inclination. Therefore, trans-fatty acids are of a more linear
form than their cis isomers, as it is shown in Figure 1 in the
case of cis and trans oleic acid.
As a result, trans-unsaturated fatty acids increase the
polarity of the cellular membrane surface and allow better
packing of the acyl-chains that lead to its solidification and
make it less functional.
Additionally, trans-fatty acids taken up from the diet are
incorporated into higher lipids such as triglycerides,
phospholipids and cholesterol esters [17]. Thus, like saturated
fatty acids, trans-fatty acids increase CETP activity, which in
turn raise LDL (Low density lipoprotein), whereas trans-fatty
acids in contrast to saturated fatty acids also lower the blood
HDL (High density lipoprotein). CETP (cholesteryl ester
transfer protein), also called plasma lipid transfer protein, is a
plasma protein that facilitates the transport of cholesteryl esters
and triglycerides between the lipoproteins. It collects
triglycerides from LDL and exchanges them for cholesteryl
esters from HDL and vice versa. The effect of trans-fatty acids
on blood LDL/HDL ratio can therefore be even more severe
than that of saturated fatty acids. LDL cholesterol participates
in the development of arteriosclerosis, whereas HDL
cholesterol is sometimes considered “good” cholesterol
because in this form cholesterol is transported to the liver for
metabolism and elimination [20]. Epidemiological studies have
also found that the consumption of trans-fatty acids increases
the risk of coronary heart disease, sudden death and possibly
also diabetes mellitus [17].
© 2009 The Chemical Educator, S1430-4171(09)0xxxx-x, Published on Web 12/29/2009, 10.1333/s00897092221a, xxxxxxaa.pdf
Molecular Structure and Chemical Bonding
Figure 1. The structure of cis and trans oleic acid.
Jason arrives at home and looks at her mother preparing a
cherry flavored jelly. He thinks to add some kiwis in it. After
several hours the jelly had not set yet. He wonders: “What did
it go wrong?” It is time for Jason to learn about the role that
the molecular structure and the chemical bonding play to the
enzymes action. Τhe main ingredient of jelly is gelatin, which
consists of collagen molecules. Each one of its molecules
consists of three polypeptide chains stratified in such a way
that form a triple helix [21]. On the other hand, the enzyme
actinidin, which is found in kiwi, is a cysteine protease and is
responsible for “breaking” the collagen peptide bond. The rest
of the enzymes that belong to the same family of proteases:
bromelain, which is found in fresh pineapple, ficin which is
found in fig and papain which is found in the exotic fruit of
papaya and flourishes in the countries of Asia and Africa, react
in a relative manner [22, 23]. The hydrolysis of the peptide
bond begins with an attack to the carbonyl carbon (C) of the
peptide bond by the sulfur atom (S) of the cysteine –SH group
(Figure 2). The proton of the histidine protonated form is then
transferred to the nitrogen atom of the attacked peptide bond,
which is broken [21].
He is sitting sad and troubled in his house living room while
watching his father adding ice to his drink. The drink
magically becomes white. Jason forgets his unsuccessful
attempt to make kiwi jelly and thinks “What kind of drink is
that and why does it become white when ice is added?” This
Greek drink is called ouzo. In the chemistry course he will
learn that ouzo is produced by the double distillation of
tsipouro and the addition of flavorings, such as anise, fennel,
ginger, cinnamon and others. These flavorings contain
anethole essence oil. The chemical formula of anethole is
C10H12O and the full chemical name is trans-1-methoxy-4(prop-1-enyl) benzene. Anethole consists mainly of the trans
isomer (99%) which has a sweet taste and characteristic odor;
cis-anethole is a toxic substance [24]. As it is shown from its
structure (figure 3) anethole is an aromatic compound with
very low solubility in water (<50mg/L).
When we add water in ouzo the alcohol dissolves in it
creating hydrogen bonds, while anethole remains insoluble and
forms a white emulsion [25].
The surprising fact that the oil droplets in a water-rich ouzo
mixture slow down their growth and form a stable liquid
dispersion was first studied by Vitale and Katz, [26] who
termed it the “ouzo effect”. The “ouzo effect” enables one to
Chem. Educator, Vol. 14, No. X, 2009
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create a dispersion of small droplets in a surrounding liquid
phase without the use of surfactants, dispersing agents, or
mechanical agitation: a phenomenon which can be of value in
many disciplines. Dispersions of oil droplets in water are
formed by the addition of water to a solution of the oil
dissolved in a solvent. This causes the oil to supersaturate and
then nucleate into small droplets. These droplets are
responsible for the cloudy aspect of the solution.
The concentration of ethanol in ouzo drink is about 40-42%
before adding extra water. Proton spectra recorded at different
ethanol concentrations show that only the free dissolved form
of the trans anethole is present above 40% of ethanol. Thus,
ouzo remains a colourless drink. Herein, a more detailed
analysis of each state of trans anethole emulsification showed
that the moment the water is added to the drink, the
concentration of ethanol is reduced and trans anethole
molecules reorganize into small aggregates of angstrom-size,
which are visible by using standard liquid NMR experiments.
Simultaneously, these small aggregates coalesce in between
them to form small micrometer-size droplets [25].
Using dynamic light scattering, Sitnikova et al. showed that
the droplets of oil in the emulsion grow via Ostwald ripening,
and that droplets do not coalesce. The Ostwald ripening rate is
observed to reduce at higher ethanol concentrations and
eventually to reduce such that the droplets stabilize in size. The
average diameter of the droplets stabilized at a value of
typically 3 micrometre [27].
As a result, the emulsion becomes stable. The stability of an
emulsion can be referred to as the resistance to the coalescence
of the emulsion’s dispersed droplets. The rate of coalescence
of droplets in an emulsion is taken as a quantitative measure of
emulsion stability. The stability of a colloidal suspension can
be explained in terms of the DVLO theory which states that the
stability is dependent on two independent interactions between
colloidal particles: the van der Waals attraction and the
electrostatic repulsion between electrical double layers of
identical sign. The theory predicts that if the potential
repulsion (PR) exceeds the absolute value of the attraction
potential (AV) by a certain value (PR – AV = W >> kT) at any
distance between the particles, the suspension will be stable.
For low values of the repulsion potential (W- kT), the
suspension will coagulate as soon as the particles approach
each other by the diffusion process. Trans anethole acts as an
emulsifying agent which stabilizes the system by reducing the
interfacial tension between the two liquids (and consequently
the thermodynamic instability of the system) and decreases the
rate of coalescence of the dispersed liquid particles by forming
mechanical, steric and/or electrical barriers around them [28].
After thinking the ouzo effect, Jason prepares to sleep. He
goes to his room, turns on the bedside lamp, he looks at the
incandescent light bulb and wonders: “what metal is placed in
the lamp in order to light and heat so much without melting?”
If his teacher was there, Jason would be taught that the metallic
bonding is interpreted by various theories among which the
theory of “free” electrons predominates. The strength of the
metallic bonding increases for the first members of each line of
the periodic table according to the number of unpaired
electrons. This could be explained based in the hypothesis that
up to 5 (V) or 6 (Cr) d electrons participate in the metallic
bonding, and after this number the remaining d electrons are so
strongly attracted by the nucleus charge that they no longer
participate in the creation of a metallic bond. The participation
© 2009 The Chemical Educator, S1430-4171(09)0xxxx-x, Published on Web 12/29/2009, 10.1333/s00897092221a, xxxxxxaa.pdf
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Chem. Educator, Vol. 14, No. X, 2009
Vlassi et al.
Figure 2. Mechanism of the actinidin action.
Figure 3. The structure of anethole.
of all d electrons ceases after tungsten (W) for the 3rd line of
the transition elements. Due to the great strength of the
metallic bonding the transition elements are hard, difficult to
melt and have high melting and boiling points. The hardest of
all is tungsten, with the highest sublimation enthalpy of all
other elements, and this is why it is used for the construction of
incandescent light bulbs and filaments [29].
Conclusions
Studying the above examples, we can only agree with the
words of Jay Ingram, (1989): “When we ignore the science of
everyday life we are much poorer. Firstly it is a type of science
that is approachable by anyone who was daunted by the class
in junior high school and high school. (Quantum theory may
be frightening, but the reason we blink is not). The most
important is the fact that life becomes more interesting when
we have a better understanding of the world that surrounds us.
I guarantee you that eating asparagus or yawning will not be
the same anymore after you have known their scientific
meaning” [3].
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© 2009 The Chemical Educator, S1430-4171(09)0xxxx-x, Published on Web 12/29/2009, 10.1333/s00897092221a, xxxxxxaa.pdf