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ORGANIC AND BIOMOLECULAR CHEMISRTY – Organic and Bio-Molecular Chemistry - Francesco Nicotra
ORGANIC AND BIO-MOLECULAR CHEMISTRY
Francesco Nicotra
Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milano,
Italy
Keywords: Organic compounds, Carbon atom, Chemical structures, Alkanes, Alkenes,
Alkynes, Aromatic hydrocarbons, Haloalkanes, Alcohols, Thiols, Ethers, Amines,
Aldehydes, Ketones, Carboxylic acids, Chemical reactivity, Carbohydrates, Amino
acids, Nucleic acids, Lipids, Fats , Oils, Waxes, Dyes, Medicinal drugs, Nutraceutics,
Polymers, Chemical separation, Structure determination, Chromatography
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Contents
1. Introduction
2. The Carbon atom
3. Structure of organic compounds
4. Classification of organic compounds, the functional groups
5. Attractive interactions and molecular recognition
6. Reactivity of organic compounds
7. Molecules of life
8. Organic compounds in the market
9. Isolation, purification and analysis of organic compounds
10. Conclusions
Glossary
Bibliography
Biographical Sketch
To cite this chapter
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Summary
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Organic and Bio-Molecular chemistry is the discipline that studies the molecules of life,
which are made by carbon atoms, and includes also all the synthetic compounds the
skeletons of which contain carbon atoms. Living organisms are “built up and organized”
exploiting compounds the skeleton of which is mainly made up of carbon atoms. The
study of these compounds, defined Natural Compounds, as far as structure, properties
and biological role is concerned, is the subject matter of Organic and Bio-Molecular
Chemistry. Chemists have been able to synthesize a great variety of new compounds
with a skeleton mainly based on carbon atoms; these new molecules also belong to the
class of Organic Compounds. The carbon skeleton of organic compounds represent the
stable scaffold, in which the presence of multiple bonds and heteroatoms, mainly
oxygen, nitrogen, sulfur, and phosphor, eventually allow the organic molecule to
perform “functions” such as molecular interactions and reactivity. For this reason these
groups are defined as functional groups and give rise to the most common classification
of organic compounds. Organic chemistry studies the structure, nomenclature, physicochemical properties and reactivity of each single class of organic compounds. Particular
attention is devoted to organic compounds of living organisms, such as carbohydrates,
amino acids and proteins, nucleic acids, lipids; they perform all structural and/or
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functional roles that allow an organism to live and reproduce. Organic compounds have
also an important role in the market, and the chemical industries strongly contribute to
the economy of industrialized countries. Many organic compounds such as polymers,
dyes, compounds for health care such as medicinal drugs and cosmetics, compounds for
food industry such as sweeteners, nutraceutics, preserving agents, emulsifiers and
stabilizers, are widely used and contribute to our quality of life. The extensive
production and use of synthetic organic compounds has generated some environmental
problems, therefore particular attention is devoted to environmentally safe production
processes and biodegradable organic polymers. Organic and Bio-Molecular chemistry
also studies how to isolate organic compounds from a mixture, how to determine the
chemical structure and how to detect purity. A variety of instrumental techniques have
been developed for these purposes; it is now possible to detect the presence of organic
compounds, even in traces, and to determine their chemical structure.
1. Introduction
Chemistry is the discipline that studies the structure, properties, and methods of
manipulation and transformation of all materials around us, from simple gases present
in the air, nitrogen and oxygen, to the strangest and most complex compounds produced
by microorganisms. Organic and Bio-Molecular Chemistry concerns in particular, as
indicated by the name, the wide variety of compounds that constitute the living
organisms; it includes however also structurally related compounds that have been
mass-produced in laboratories and by industry in the 20th century.
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The origin of modern Organic Chemistry can be dated at the beginning of the 19th
century, when scientists such as Gay-Lussac (1810) and Berzelius (1814) developed
methods of analysis of the compounds derived from living organisms, allowing a
systematic study which put into evidence the common characteristics of these
compounds, that have been classified as “organic compounds”. For a long time it was
believed that organic compounds were generated in Nature by a sort of magic “vital
force”, despite the fact that in 1828 Wölher was able to demonstrate that the urea
produced in the laboratory by heating ammonium cyanate, an inorganic compound, was
identical to the urea of natural origin.
Looking for a common characteristic of organic compounds, it was very soon clear that
there is a relevant difference in chemical composition between them and inorganic
compounds. Rocks are mainly made up of Oxygen (O) and Silicon (Si) atoms (see
Table 1), whereas the structure of compounds of living organisms is mainly made with
Carbon (C) atoms. Table 1 describes the percentage of the different elements present in
the inanimate earth with respect to the human body. Considering that one of the most
abundant compounds in the human body is water (H2O), it is clear from the Table that
the most abundant element in the structure of organic compounds is Carbon.
Earth
Element
O
Si
Al
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%
47
28
7.9
Human body
Element
%
H
63
O
25.5
C
9.5
ORGANIC AND BIOMOLECULAR CHEMISRTY – Organic and Bio-Molecular Chemistry - Francesco Nicotra
Fe
Ca
Na
K
Mg
Ti
H
C
4.5
3.5
2.5
2.5
2,2
0.46
0.22
0.19
N
Ca
P
Cl
K
S
Na
Mg
1.4
0.31
0.22
0.08
0.06
0.05
0.03
0.01
Table 1: Percentage of the different elements present in the inanimate earth with respect
to the human body
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Organic Chemistry is therefore the chemistry of carbon-containing compounds, no
matter if they are natural or synthetic.
The evolution of Organic Chemistry has been impressive, there are practically no limits
as to what can be synthesized in a laboratory; apart for very complex natural
compounds, a large number of new compounds have been synthesized for different
purposes. Organic compounds have a place in our everyday life; they constitute many
useful materials such as plastic or fibers; they are present in food and beverages (which
by the way are by definition organic compounds) as sweeteners, vitamins, flavors,
coloring agents, emulsifiers, preservatives; they are used for health care, as medicinal
drugs or cosmetics.
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Starting from petrol, which is presently the cheapest and most abundant reserve of
organic compounds, a potentially infinite number of different molecules can be
synthesized, by exploiting the great variety of chemical reactions that have been
developed since the 21st Century, and progress in the techniques of purification and
structural determination. On the other hand, the molecular mechanisms of life, all
involving organic compounds, from complex proteins to very small neurotransmitters
such as acetylcholine or noradrenaline, have been largely elucidated. Proteins,
carbohydrates, nucleic acids, lipids, products of the secondary metabolism, and more in
general organic compounds of the biological systems, are specifically defined “biomolecules” and the branch of organic chemistry that studies the nature of these biomolecules and their behavior in the organism, is defined “bio-molecular chemistry”
2. The Carbon Atom
The Carbon atom is the main constituent of organic molecules, as shown in Table 1,
whereas the Silicon atom is the main component of rocks. Why? Why are rocks mainly
built-up of Silicon and Oxygen atoms whereas Nature has selected the Carbon atom for
living organisms? Silicon and Carbon have a common feature: they are “tetravalent”, in
other words they are like scaffolds that can be elongated in four directions. Silicon and
Carbon atoms can establish four molecular bonds, represented with a line in Figure 1,
each of which links a different atom. Four linkages with different atoms is the highest
possibility for the most abundant elements present in the earth; hydrogen and chlorine
are monovalent, they can establish only one linkage; oxygen is bivalent, it establishes
two linkages; nitrogen, boron and aluminum are trivalent, they can establish three
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linkages with different atoms. Therefore silicon and carbon, the two abundant
tetravalent elements, are the most efficient scaffolds to build up tridimensional
molecular structures. There is however an important difference between silicon and
carbon: the energy of C-C linkage is around 80-90 kcal/mol, whereas the Si-Si linkage
is much weaker, 53 kcal/mol, which makes it very unstable. On the other hand, the Si-O
bond is very strong (108 kcal/mol), therefore very stable molecular architectures can be
generated intercalating Si and O atoms as shown in Figure 1 for silicates. This kind of
structure is so stable, let us say “static”, to be inadequate for living organisms which
require more “dynamic” compounds. Living organisms generate fructose, an organic
compound with a six carbon atom chain, from carbon dioxide and water, in a process
defined as photosynthesis which exploits the energy of the sun. Fructose undergoes
metabolic transformations to generate other organic compounds. It is clear therefore that
organic molecules must be “dynamic”, as they must be generated (biosynthesized) and
transformed (metabolized) by cleavage of some bonds and formation of new ones. The
carbon atom is much more suitable for this purpose, 80-90 kcal/mole of the C-C bond is
the strength of choice, not too strong and not too weak; therefore it has been selected in
Evolution to generate organic compounds. Palmitic acid, in Figure 1, present in palm
tree oil, is an interesting example of an organic compound in which sixteen carbon
atoms are linked together generating a long chain.
Figure 1: Silicon and carbon atoms are scaffolds that can elongate in four different
directions generating four linkages, the two examples refer to the general structure of
silicates (the oxygen atoms can be linked to other silicon atoms, for further elongation,
or hydrogen atoms)
2.1. The Carbon Atom Building Blocks: Hybridizations
The carbon atom is tetravalent and, as stated before, is a building block that can give
rise to four different bonds. These four bonds are oriented in the space at 109.5°, as
shown in the first example of Figure 2. However the carbon atom is a very ductile and
dynamic building block; it can assume different “hybridizations” that make bonds in
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different directions in space. In the so called sp3 hybridization (first example in Figure
2) the carbon atom generates linkages in four directions at 109.5° exploiting the so
defined “orbitals” (spaces that can be occupied by electrons and therefore can generate
molecular bonds). Alternatively, in the so called sp2 hybridization (second example in
Figure 2), the carbon atom generates linkages in three directions at 120°. Finally, in the
so called sp hybridization (third example in Figure 2), the carbon atom generates
linkages in two directions at 180°. It is interesting to note that 109.5°, 120° and 180° are
the angles that allow respectively four, three and two linkages to be at the highest
reciprocal distance.
Figure 2: The different hybridization of carbon atom allows it to generate bonds in
different directions in space.
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2.2. Single and Multiple Bonds
Figure 3: Ethane has two carbon atoms with sp3 hybridization, which generate four σbonds each. Ethylene has two carbon atoms with sp2 hybridization, generating each
three σ-bonds and one π-bond. Acetylene has two carbon atoms with sp hybridization,
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ORGANIC AND BIOMOLECULAR CHEMISRTY – Organic and Bio-Molecular Chemistry - Francesco Nicotra
generating each two σ-bonds and two π-bond. 1,2-Butadiene has one carbon atom
hybridized sp, generating one σ-bonds and one π-bond with each of the two carbon
atoms linked to it.
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The linkages so far described, that join the atoms like a line starting from the centre of
each atom, are defined sigma (σ) bonds. Without entering into details on the nature of
the orbitals that generate the molecular bonds, in the sp2 hybridization the carbon atom
will generate also a second bond, defined pi-Greek (π) bond, with one of the three
atoms with which it is linked; in other words a double bond is generated (see ethylene in
Figure 3). The carbon atom with an sp hybridization will create two more bonds (π
bonds) with one of the two atoms linked to him, therefore generating a triple bond (see
acetylene in Figure 3). Alternatively, the sp hybridized carbon atom can generate two
double bond (see 1,2-butadiene in Figure 3). In each case the carbon atom generates in
total four bonds.
The hybridization of the carbon atoms is a dynamic feature, which means that in a
chemical reaction a single carbon atom can change the hybridization, and consequently
the geometry of the linkages and the type of bounds.
3. Structure of Organic Compounds
Once we know the geometry of the three carbon atom building blocks, we can start to
build and represent the organic molecules emphasizing their size and geometry. In order
to do that we need a conventional method to draw the three-dimensional structures in
two dimensions on a sheet of paper.
3.1. Graphical Representation of the Structures of Organic Compounds
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Historically, the first way to represent the structure of organic compounds was simply to
draw the four linkages established by a carbon atom with four lines at 90°, linking the
neighboring atoms, as in Figure 1 for palmitic acid. This representation is still used,
although it does not respect the correct angles of the tetrahedral sp3 carbon atom
(109.5°). However, it is also time consuming for large molecules such as palmitic acid.
The evolution of the methods of graphical representation of organic molecules has
followed two different requirements, that of simplicity and the need to give information
on the real geometry of the molecule, if required. Therefore, different conventional
representations find application depending on what we want to highlight. In order to
simplify the representation of an organic compound, the lines representing the bonds
can be omitted, like in Figure 4B for a simpler representation of palmitic acid. A further
simplification allows us to represent a sequence (chain) of CH2 with just one CH2 in
brackets, with a subscript number indicating the amount of CH2 in the chain (Figure
4C). Another way to represent organic molecules, which simplifies the drawing as much
as possible, and is therefore useful and often indispensable to represent molecules with
very complex structures, omits the symbols of carbon and hydrogen atoms. The
molecule is represented with a sequence of lines, as reported in Figure 4D for palmitic
acid, each angle and extremity represent a carbon atom linked to the hydrogen needed to
complete the structure.
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ORGANIC AND BIOMOLECULAR CHEMISRTY – Organic and Bio-Molecular Chemistry - Francesco Nicotra
Figure 4: Conventional representations of organic compounds. In A all the bonds and
atoms are represented, but the real geometry of the bonds is not respected. In B the
bonds are omitted for simplicity; in C the representation of the carbon chain is
simplified, in D the symbols of the atoms in the carbon chain are omitted for simplicity.
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This last representation can be adopted to show the real geometry of the bonds of a sp3
hybridized carbon atom, two of which are represented by the two lines on the plane,
drawn at about 109.5°. The other two bonds, one of which is directed towards the
observer and the other to the back of the plane, can be represented respectively with a
wedge and a hatched line (Figure 5). Another representation of a sp3 hybridized carbon
atom, which describes the geometry of the bonds, is the historical conventional method
invented by Emil Fisher and still used for amino acids and sugars. In the Fisher
representation the four bonds are drawn like a cross, with the carbon atom in the centre.
The horizontal lines are conventionally oriented towards the observer (out from the
plane), whereas the vertical lines are conventionally oriented back to the plane, opposite
to the observer (Figure 5, right).
Figure 5: Conventional representations of the sp3 hybridized carbon atom, describing
the real geometry of the molecule.
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3.2. Different Shapes that a Molecule can assume: Conformations
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In Figure 4 palmitic acid has been represented as a long bar. Is this true? Is it a rigid
molecule or it is flexible like a string? The study of the shape of a molecule, in other
words, the orientation of the atoms in the space, requires further information. The
rotation around single (σ) bonds is generally allowed, therefore a molecule such as
palmitic acid, in which each C-C bond is a single bond, is like a piece of string that can
be turned as we like and assume an almost infinite series of orientations in the space. To
be more precise, let us study the case of a simple molecule with four carbon atoms like
butane (Figure 6), the rotation around the single bond will generate all possible angles
between the two CH3 at the extremity of the chain, which correspond to different sizes
of the molecule, defined “conformations”. Some conformations however are more
stable than others. In the conformation described at the left in Figure 6, which is defined
“anti conformation”, the two CH3 are at 180° (as far as possible), whereas in the
conformation represented at the right, which is defined “gauche conformation”, the two
CH3 are at 60° (much closer). The anti conformation is the most stable among all the
possible conformations because the repulsive interaction between the CH3 (or any other
group in the case of a different molecule) is minimized at 180°.
Figure 6: Rotation around the σ-bond allows the molecule to assume an infinite number
of conformations, a couple of which are reported for butane.
The presence of a double bond in a molecule generates a conformational rigidity: the
rotation around a π-bond is not allowed. Nature takes advantage of the decreased
flexibility of compounds presenting a double bond. To make an example of the
macroscopic difference that the presence or absence of a double bond can generate, oil
and butter have essentially the same chemical structure (triglycerides, see Section 7.4.1)
with the only difference that oil contains a substantial amount of double bond in its long
chain components (fatty acids such as oleic acid, Figure 7), which prevent the ordered
aggregation of the linear carbon chains that determine the solid state of butter. Figure 7
shows the most stable conformation of palmitic acid, which is linear and generates
ordered aggregates with molecules of the same type, and oleic acid in which the double
bond prevents a linear conformation and therefore an ordered aggregation.
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ORGANIC AND BIOMOLECULAR CHEMISRTY – Organic and Bio-Molecular Chemistry - Francesco Nicotra
Figure 7: Palmitic acid and oleic acid. The double bond of oleic acid prevents a totally
linear conformation.
3.3. Asymmetry of some Organic Molecules: Chirality and Stereoisomers
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A carbon atom linking four different elements or groups, such as that represented by the
cross in Figure 5, is asymmetric (stereogenic, see Stereochemistry), and the molecule to
which it belongs is defined “chiral”. A different molecule can be generated by changing
the reciprocal position of two substituents. Figure 8 represents at the left the same
molecule represented in Figure 5, and on the right different, non super-imposable,
molecules which differ only by the orientation of the group in space. Compounds with
these reciprocal structural characteristics are defined stereoisomers (stereo refers to
space, and isomer refers to a structural similarity, same number of atoms, differently
positioned). The two different orientations of the elements and groups at the stereogenic
carbon atom are defined configurations.
Figure 8: Two stereoisomers, molecules that differ only in the orientation of atoms or
groups in the space. The two compounds represented are mirror images.
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The two compounds represented in Figure 8 have opposite configurations, they are
stereoisomers. In particular, the molecules of the two compounds in Figure 8 are mirror
images, a geometrical property that make them identical in their chemical and physical
properties, and only an asymmetric “instrument” can discriminate between them, they
are defined enantiomers. The example of the hands is pertinent; the two hands, left and
right are non super-imposable and are mirror images. Only an asymmetric glove (the
left is different from the right) allows us to discriminate between them, it fits only one
of the two hands.
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Molecular asymmetry is widely spread in Nature. Amino acids that constitute the
proteins (proteogenic) are all chiral except glycine. The configuration of proteogenic
amino acids is constantly “L”, a conformational descriptor that, according to the Fisher
projection formulas, is given to the amino acid that in the representation shown in
Figure 9 presents the nitrogen atom on the left. More in detail, the Fischer projection
formula requires that the carbon chain is drawn in vertical with the most oxidized
carbon atom at the top. The chiral carbon atom is then represented with a cross, and if
the “main” group is on the left, the conformational descriptor is L, if it is at the right, the
descriptor is D. This convention is still used for amino acids and sugars, but for all the
other organic compounds, a newer convention is used, the conformation descriptors
being R and S. For a detailed description see Stereochemistry.
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It is interesting to mention that bacteria contain D-alanine, which they use to generate
their cell wall. D-Alanine is therefore an important target for medicinal chemistry,
indispensable for bacteria and absent in our organism. Penicillins, which mimic two
molecules of D-alanine linked together, are able to inhibit the biosynthesis of the
bacterial cell walls, without interfering with the human metabolism.
Figure 9: L-Alanine and D-Alanine, the first is the proteogenic amino acid whereas the
second is present in the bacterial cell wall.
A dramatic example of the different behavior of two enantiomers (mirror images),
comes from the drug Taledomide that was used in Europe and Canada in the 1960s for
the treatment of nausea in pregnant women. The drug was administered as a mixture of
the two mirror image stereoisomers, although only one of the two was responsible for
the anti-nausea activity, because separation was difficult and it was believed that the
inactive stereoisomer was safe. Unfortunately it was mutagenic and anti-abortive, and
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was responsible for the birth of deformed infants with underdeveloped limbs. This event
led to new restrictions in the commercialization of drugs, and in fact stereochemical
purity is now required.
4. Classification of Organic Compounds, the Functional Groups
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The structure of organic compounds, as shown in the case of palmitic acid, is made by a
skeleton of carbon atoms, to which hydrogen atoms are linked to complete the structure
(the carbon tertavalence). Palmitic acid however presents at one extremity a different
structural situation: the carbon atom links two oxygen atoms, one with a double bond
and the other with a single bond; this latter oxygen atom completes the bivalence
linking a hydrogen atom. This arrangement of atoms is responsible for some “functions”
of palmitic acid, such as the acidity, the possibility to link other molecules or the
formation of micelles in alkaline aqueous solution; therefore this arrangement of atoms
and bonds is a “functional group”. In general, the skeleton of organic compounds is
mainly made up of carbon atom chains or cycles, whereas the functions are mainly due
to groups that present atoms different to carbon and hydrogen (defined heteroatoms),
and/or by multiple bonds. These groups are therefore defined functional groups.
Organic compounds are generally classified according to the functional groups present
in their structure. The name alcohol, for example, is well known; it refers to an organic
compound in which the carbon atom is linked to an oxygen atom, which in turn links a
hydrogen atom. The alcohol present in beverages, ethanol, is made by a chain of two
carbon atoms, one of which links an oxygen atom bearing a hydrogen atom: CH3CH2O-H. A carbon chain can be represented more in general with the letter R, therefore the
general structure of alcohols is R-O-H. The main classes of organic compounds are
reported with their names in Table 2.
N
Alkanes
R
R
U
R C
R
R can be H
Alkenes
R
R
C C
R
R
R can be H
Alkines
R
C
C R R can be H
Alkyl halides
R
R C
R
Cl
R can be H, Cl can be Br, I
©Encyclopedia of Life Support Systems (EOLSS)
Amines
R
R N
R one or two R can be H
Aldehydes
R
C O
H
R can be H
Ketones
R
C O
R
Carboxylic acid
O
R C
OH R can be H
ORGANIC AND BIOMOLECULAR CHEMISRTY – Organic and Bio-Molecular Chemistry - Francesco Nicotra
Alcohols
R
R C
OH
R
Ethers
R
R C
Carboxylic esters
O
R C
O R' R can be H
R can be H
Amides
O
R
O
R
Thiols
R
C
R
R
R
C
N R'
R'
R and R’ can be H
R can be H
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Nitriles
R C
R
SH
R
Thioethers
R
R
R C
C
S
R
C
N
R can be H
R
R
R can be H
Table 2: Main classes of organic compounds
4.1. Alkanes
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Compounds made up exclusively of carbon and hydrogen atoms, and presenting only
single bonds, are defined alkanes. Methane (CH4), propane (CH3CH2CH3) and butane
(CH3CH2CH2CH3), used at home for heating or cooking, are examples of alkanes.
Polyethylene is a polymer formed by a chain of –CH2-, and therefore belongs to the
class of alkanes. Alkanes can be linear, branched, cyclic an even polycyclic. The main
source of alkane is petroleum, or crude oil, a fossil fuel formed over many thousands of
prehistoric plants. Commercial products obtained by the fractional distillation of crude
oil contain alkanes with a different number of carbon atoms. Gasoline for example, the
motor fuel, is a mixture of alkanes with 5-12 carbon atoms, whereas Diesel contains
alkanes with 15-20 carbon atoms. Lubricant oils are made with a mixture of alkanes
containing 20-30 carbon atoms, and asphalt used as road surface material contains
alkanes with more than 40 carbon atoms.
4.2. Alkenes
Compounds presenting one or more carbon-carbon double bonds are defined alkenes.
The simplest alkene is ethylene, CH2=CH2, which is very important as a starting
material for the production of polyethylene and in ripening of fruit. Some plants
generate small quantities of ethylene during the ripening of their fruits; therefore this
alkene is used to ripen fruit, which has been picked green to be transported intact to
destination. A great variety of natural products contain carbon-carbon double bonds. We
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have already seen the example of oleic acid (Figure 7) in which the presence of a double
bond alters the linear geometry of the molecule. A great number of fragrant substances
extracted from plants such as limonene or γ-terpinene (Figure 10), respectively
components of the essential oil of lemon and coriander, belong to the class of alkenes.
β-Carotene, the pigment responsible for the orange color of carrots, is another
interesting example of a naturally occurring alkene; it contains 11 carbon-carbon double
bonds (Figure 10).
Figure 10: Examples of alkenes of natural origin.
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It is interesting to mention that, in the light of the fact that the rotation around a double
bond is not allowed, two different molecules (once more defined stereoisomers, see
Section 3.3) can be generated depending on the geometry of the double bond. In oleic
acid (Figure 7) the two chains are located on the same side of the double bond, a
geometry that is defined with the letter Z (from the German term zusammen: together).
The other stereoisomer, in which the substituents at the double bonds are located on the
opposite side, is not present in olive oil; the geometry of its double bond is defined E
(from the German word entgegen: opposite).
4.3. Alkynes
Compounds presenting carbon-carbon triple bonds are defined alkynes. The best known
example of alkyne is acetylene, which has been used as a combustible for lamps.
Alkynes are relatively rare in living organisms, and often present physiologically
relevant activities. Ichtyotherol (Figure 11), which contains three C-C triple bonds, is
the active principle in the plant extract used by natives in the Amazon region to poison
their arrowheads.
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Figure 11: The structure of ichtyotherol, active principle of the plant extract used by
natives in Amazon to poison their arrowheads.
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The example in Figure 11 put into evidence the limit of the classification of organic
compounds according to the functional group they present. Ichtyotherol has not only
three carbon-carbon triple bonds, but also a carbon-carbon double bond, and a carbon
linked to an –O-H; therefore it is not only an alkyne, but also an alkene and an alcohol.
The classification of organic compounds according to the functional group is however
very useful to study the properties and the behavior of each functional group in a
molecule.
4.4. Aromatic Hydrocarbons
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Alkanes, alkenes and alkynes, which possess only carbon and hydrogen atoms, are also
called hydrocarbons (from hydrogen-carbon).
Figure 12: A) Benzene, naphtalene and anthracene, examples of aromatic hydrocarbons;
B) pyridine, purine, pyrrole, furan, thiophene, imidazole, indole and purine, examples of
heteroaromatic compounds
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Benzene (Figure 12) presents only carbon and hydrogen atoms, and therefore is a
hydrocarbon. Benzene however has a different chemical behavior (reactivity) due to a
peculiar stability of planar cyclic compounds with an alternation of double and single
bonds and with a well defined (4n+2), n = 0,1, 2, 3,… number of electrons in the πorbitals. These compounds are defined aromatic compounds (an exhaustive definition
of aromatic compounds is not possible at this level). Naphtalene and anthracene are
other examples of aromatic hydrocarbons.
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A wide variety of aromatic compounds contain also heteroatoms in the cycles that
characterize and determine their aromacitity. These compounds are defined
heteroaromatic compounds; the most important are reported in Figure 12 B. Pyridine
and purine are six member cyclic compounds respectively with one or two nitrogen
atoms instead of the carbon atom of benzene. Pyrrole, furan and thiophene are cycles
containing five atoms, one of which is, respectively, nitrogen, oxygen and sulfur,
whereas imidazole contains two nitrogen atoms (Figure 12B). Indole and purine are
bicyclic compounds, the first with just one nitrogen atom in one cycle, whereas the
second contains four nitrogen atoms (Figure 12 B). From these examples it is clear how
big is the structural variance in aromatic compounds. Nature exploits this variance for
many functions: some derivatives of purine and pyrimidine are constituents of nucleic
acids (see below); indole and imidazole are present in the structure of two amino acids
that constitute the proteins, the structure of pyridine is part of NAD, an important
enzymatic cofactor that allow to establish the biological oxidation and reduction.
4.5. Haloalkanes
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Haloalkanes are a class of organic compounds containing the carbon-halogen bond.
These compounds are rare in Nature because their high reactivity (except for fluorides)
makes them dangerous for living organisms. Iodomethane, CH3I, for example is
carcinogenic. On the contrary, when the halogen is linked to an aromatic skeleton, the
compound is very stable, often so stable that it cannot be biodegraded. A relevant
example of this behavior is DDT (Figure 13) which was widely used in the past as a
pesticide, but caused serious environmental problems due to its stability and toxicity.
Another example of a stable and very dangerous halogenated compound is dioxin
(Figure 13).
Figure 13: The structures of DDT and dioxin, two environmentally dangerous
halogenated compounds.
Haloalkanes are used as solvents and in the production of polymers such as PVC
(polyvinyl chloride) and Teflon (Figure 14)
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Figure 14: The structure and PVC and Teflon, two halogenated polymers
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Fluoroalkanes have a different behavior: they are not reactive like the other haloalkanes,
furthermore they are not toxic or flammables. Chlorofluoroalkanes (CFC or Freon) are
the most known, widely used as fluids for refrigeration and in aerosols. However in
1974 it was demonstrated that these compounds are responsible for the destruction of
ozone in the atmosphere. As a consequence of these scientific results, in 1987 the
protocol of Montreal was approved by the United Nations that strongly limits the use of
these compounds.
4.6. Alcohols
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Alcohols are a class of organic compounds containing the -O-H (hydroxyl) functional
group.
Figure 15: Sucrose contains eight hydroxyl groups, glycerin three hydroxyl groups.
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The alcoholic function is one of the most widely present in natural compounds. Sugars
for example contain numerous hydroxyl groups, as shown in Figure 15 for sucrose, the
table sugar, which contains 8 hydroxyl groups.
Another widely used alcohol is glycerin (or glycerol) which is the main component of
the cosmetic creams. Cholesterol also contains an alcoholic function (Figure 15).
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The hydroxyl function of alcohols is like a hook that can be used to link a different
molecule, exploiting the reactivity of the hydroxyl group with other functional groups,
such as a carboxylic acid or an aldehyde. The hydroxyl group of cholesterol for example
is the hook to link a fatty acid (like palmitic acid) or a sugar, in order to tone its
hydrophilicity. The hydroxyl group is also one of the functional groups of choice for the
reactivity; it can be oxidized, it can be eliminated as a molecule of water generation a
double bond, it can be substituted. In other words it is a “first actor” in the metabolic
processes and in synthetic chemistry.
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When the hydroxyl group is linked to the aromatic ring of benzene, the alcohol is
defined phenol. Phenols are important components of natural products, such as salicylic
acid, or morphine (ring A), or estradiol (Figure 16).
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Figure 16: Phenol and some natural products containing the phenol entity.
4.7. Thiols
When a sulfur atom replaces the oxygen of alcohols, the compounds are named thiol.
The main characteristic of most thiols is the bad smell. Ethanthiol (HS-CH2CH2-SH) for
example is added in traces to methane in order to warn in case of accidental emission of
this gas, which is odorless. The thiol group has a strong tendency to generate a sulfursulfur linkage: R-S-S-R with another thiol. This process is particularly important in
proteins, in which two units of cysteine, an amino acid containing the thiol group, can
link together and generate a disulfide bridge which turns the protein chain (Figure 17)
and therefore contribute to the folding of proteins. This process does not occur with
alcohols because the oxygen-oxygen bond, present for example in hydrogen peroxide
H-O-O-H, is very unstable and generates radicals.
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ORGANIC AND BIOMOLECULAR CHEMISRTY – Organic and Bio-Molecular Chemistry - Francesco Nicotra
Figure 17: In a protein chain the linkage of two thiol units, coming from cysteine,
induce a turn of the protein chain.
4.8. Ethers
Ethers, R-O-R, are formally generated by two alcohols by loss of a molecule of water.
More generally, when two equal or different alkyl groups R are linked through an
oxygen atom, an ether is generated. Among the ethers, diethyl ether CH3CH2-OCH2CH3, generally called simply ether, is a well known anaesthetic and highly
flammable compound. Ethers are particularly stable molecules in which the oxygen
atom contributes to increase the polarity, useful for their use as solvents, and the
capacity to bind metal cations. The system of transport of sodium, potassium and
calcium cations across the cell membranes is based on this type of binding.
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4.9. Thioethers, Disulfides and Trisulfides
Figure 18: Thioethers, disulfides and trisulfides responsible for the flavor of garlic and
onions.
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Thioethers, R-S-R are the analogues of ethers in which a sulfur atom substitutes the
oxygen. The stability of the sulfur-sulfur linkages allows the existence of disulfides RS-S-R, trisulfides R-S-S-S-R, and so on (Figure 18). These sorts of compounds are
present in essential oils of garlic, onion and cabbages, and are responsible for their
flavor (Figure 18).
4.10. Amines
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Organic compounds formally derived from ammonia NH3 by substitution of one, two or
three hydrogen atoms with carbon atoms are defined amines. R-NH2, is defined as a
primary amine; R2NH, is a secondary amine, and R3N is a tertiary amine. Amines are
basic compounds, they are able to capture a proton (H+) giving rise to the corresponding
ammonium salts (RNH2 + H+ → RNH3+). This is a most useful behavior of amines
that is exploited both in metabolic processes and in synthetic chemistry as soft bases.
Besides that, the primary or secondary amino group, like the hydroxyl group, is an
important hook through which a second molecule can be connected. Aldehydes, ketones
and carboxylic acids are functional groups connectable with primary and secondary
amines.
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The presence of a hydrophobic R group makes amines insoluble in water, whereas their
conversion in ammonium salts converts them into hydrophilic species due to the
positive charge on the nitrogen atom. This behavior allowed the easy isolation of natural
occurring amines with physiological properties from herbs extracts. Treatment of the
pulp obtained from herbs with an acidic aqueous solution permits the isolation of water
soluble natural components, among which the ammonium salts. Then, treatment of the
aqueous extract with an alkaline (basic) solution results in the precipitation of the
amines, which is insoluble in water. Historically, the natural compounds isolated
following this procedure have been defined alkaloids. A great variety of alkaloids have
shown significant physiological activities; examples are nicotine, atropine, cocaine,
serotonin (Figure 19) or morphine (Figure 16).
Figure 19: Examples of alkaloids, compounds of natural origin containing an amino
group.
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4.11. Aldehydes and Ketones
The carbon-oxygen double bond (C=O) is defined carbonyl group. The carbonyl group
is present in different classes of organic compounds, which vary depending on what is
linked to the C=O. As a matter of fact, the reactivity of compounds containing a
carbonyl group changes if it links only with hydrogen or carbon atoms, or if it links with
a heteroatom. If the carbonyl group links two hydrogen atoms or one hydrogen atom
and one carbon atom, the functional group is defined aldehyde. If the substituents are
two carbon atoms, the functional group is defined ketone.
Figure 20: Examples of aldehydes
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Aldehydes and ketones present a very similar chemical behavior. Aldehydes however
are generally less stable and can be easily oxidized to carboxylic acids, whereas ketones
are not. Among the aldehydes, formaldehyde, the first member of the class, with only
one carbon atom, is used as disinfectant. Benzaldehyde is responsible for the flavor of
almonds, and retinal is involved in the mechanism of vision (Figure 20). Vanillin, the
flavor isolated from the vanilla bean, contains three functional groups, an aldehyde, e
phenol, and an ether (Figure 20).
The most known ketone is probably acetone, which is used as solvent. Much more
complex ketones are widely present in Nature, such as muscone, the main component of
the fragrance of musk, and steroidal hormones such as testosterone and progesterone
(Figure 21)
Figure 21: Examples of ketones
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As reported before, aldehydes and ketones are able to link alcohols and primary and
secondary amines.
4.12. Carboxylic Acids, Esters and Amides
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Carboxylic acids are organic compounds containing the –COOH functional group, in
which the carbon atom links one oxygen with a double bond, and the other oxygen with
a single bond, see palmitic acid in Figure 1. The best known example of carboxylic acid
is probably acetic acid, CH3COOH, the component of vinegar obtained by microbial
(acetobacter) oxidation of ethanol in wine. As indicated by the name, carboxylic acids
have acidic properties, by treatment with a base they generate the corresponding salt
(RCOOH + NaOH → RCOO- Na+ + H2O). Salts of carboxylic acids are soluble in
water, even tough R is a long chain. In this case they form micelles, that are very small
aggregates in the internal part of which the hydrophobic long chains find place whereas
the ionic COO- extremity constitute the external hydrophilic part. These micelles are
soluble in water and at the same time can dissolve lipophilic compounds, such as fats
and oils, in the internal lipophilic part. Treatment of fats with NaOH, or other alkali, is a
process known since ancient times as saponification, which generates soaps, salts of
fatty acids (such as palmitic acid, Figure 1), which constitute fats and oils.
Figure 22: Triglyceride (a fat) and the constituent molecules, glycerol and three fatty
acids.
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The most relevant behavior of carboxylic acids is their ability to link other functional
groups, such as alcohols or primary and secondary amines, to generate respectively
esters or amides. This behavior is widely exploited by Nature, for example in the
production of fats or proteins. In the first case three long chain carboxylic acids with an
even number of carbon atoms (fatty acids) link the three hydroxyl groups of glycerol
generating a triglyceride (a fat) (Figure 22).
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In the second case many amino acids, natural compounds containing an amino group
and a carboxylic acid in the same molecule, generate a chain by sequential linkages of
the two complementary functional groups, the carboxylic acid and the amino group
(Figure 23).
Figure 23: Amino acids are the monomers that constitute proteins.
Nylon, a fiber the commercial name of which derives by combining New York-NY and
London LON, NYLON the two places of the ICI company where the substance was first
synthesized, is made approximately in the same way. In Nylon-66 a dicarboxylic acid
and a diamine, both containing six carbon atoms, are linked together in a reiterative way
to form the polymer which takes the general name of polyamide (Figure 24).
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Figure 24: Nyon-66 and its components, a dicarboxylic acid and a diamine.
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Aspirin (Figure 25) is an example of organic compound containing a carboxylic acid
and an ester; it derives from salicylic acid (Figure 16) by esterification of the hydroxyl
group with acetic acid.
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Figure 25: Aspirin contains a carboxylic acid and an ester group.
5. Attractive Interactions and Molecular Recognition
Organic molecules interact with themselves, with other organic molecules, with water,
with inorganic compounds, depending on their structure. These interactions, that can be
attractive or repulsive, are responsible for the properties of organic compounds, such as
their physical state (solid, liquid or gaseous), their solubility, the possibility to generate
aggregates, the folding properties, the molecular recognition phenomena.
The attractive interactions are due to the following weak bonds:
1) ionic interactions, occurring when the compounds present opposite charges
2) dipole-dipole interactions, occurring when the molecules present a dipole
moment, generated by elements of different electronegativity. In organic
compounds, the carbon-heteroatom bonds generate a dipole moment.
3) Hydrogen bonds, occurring between a hydrogen atom bonded to an
electronegative element (such as halides, oxygen, nitrogen) and an
electronegative element of another (or even the same) molecule.
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4) London forces. Compounds which do not present dipole moments perform very
weak attractive interactions; this is due to the motion of electrons that generate
temporary dipole moments.
In general, the polar part of a molecule interacts attractively with polar compounds,
such as water (hydrophilic interaction). On the contrary the hydrophobic part of a
molecule interacts attractively with hydrophobic compounds, such as hydrocarbons
(hydrophobic interaction). The example of soap well exemplifies this concept. The long
hydrophobic chains of fatty acid salts perform hydrophobic interactions with themselves
inside the micelle, whereas the polar carboxylic group at the surface of the micelle
interacts with water.
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Molecular interactions are at the basis of Life. Any message in our organism, such as
cell adhesion or physiological responses, any mechanism of living organisms, such as
the transmission of genetic information or enzymatic processes, occur via molecular
recognition phenomena.
6. Reactivity of Organic Compounds
Organic compounds undergo transformations in the organisms (the metabolism), and
can be modified in laboratory experiments, in other words they can react. These
reactions occur according to defined roles, in a certain period of time, and when the
required amount of energy is provided. The roles that define how and why organic
compounds react, depending on the functional groups present in the molecule, are
defined as “mechanism of the reaction”. The parameters of time for a chemical
reaction are defined “kinetic of the reaction”. The energy required to perform a
reaction concerns the “thermodynamics of the reaction”.
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Understanding of the mechanisms, the kinetic and the thermodynamic aspects of the
different organic reactions allowed the development of synthetic chemistry, which is
our capacity to transform molecules, joining them, cleaving them in smaller fragments,
changing the nature of their functional groups, to produce whatever organic compound
we want.
In each reaction there is an intermediate situation in which a bond starts to break in
order to allow the formation of a new one. This situation, defined transition state of the
reaction, corresponds to the higher level of energy that the system must overcome in
order to react. Only the fraction of molecules that possess an amount of energy equal or
higher than this barrier, defined activation energy, can overcome the barrier and
generate the product. An increase in temperature stimulates the kinetic energy of the
molecules and therefore the fraction of them that can react; therefore any reaction is
faster at higher temperatures. Living organisms however cannot increase the
temperature when and where they need to perform a chemical reaction; they use a
different strategy, exploit some “machineries” that are able to stabilize the transition
state of the reaction, therefore lowering the activation energy. This phenomenon is
termed as catalysis, and the machineries that allow stabilization of the transition state,
and consequent reduction of the activation energy, are defined catalysts. The biological
catalysts are called enzymes. Living organisms perform their metabolic reactions using
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enzymes, which accommodate the organic compound in a sort of mould, called active
site. The active site has a particular affinity for the transition state of the reaction,
which therefore is stabilized; this stabilization results in a lowering of the activation
energy. Catalysis is widely used in laboratory and industrial processes, in order to
accelerate the reactions, save energy and perform reactions that otherwise are not
practicable. Most industrial reactions exploit catalysts, which very often contain metal
derivatives. Chiral catalysts allow us to produce only one stereoisomer when a
stereogenic carbon is generated in the reaction. In this way living organisms are able to
generate chiral molecules, such as L-amino acids. Enzymes are by definition chiral
catalysts, performing stereoselective reactions, in other words reaction in which only
one (or mainly one) stereoisomer is generated. Stereoselective catalysts are very
important in laboratory and in industrial processes as well. The example of Taledomide
shown before (Section 3.3) clearly indicates how important it is to produce only (or
mainly) one stereoisomer.
Figure 26: Sulfonamides mimic p-aminobenzoic acid, one of the biosynthetic precursors
of folic acid, the carboxylic acid being substituted by a similar, but ineffective
functional group.
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The understanding of reaction mechanisms occurring in biological processes, allows us
to design inhibitors of such processes. This is one of the strategies adopted in drug
research. To give an example, sulfonamides are able to inhibit the biosynthesis of folic
acid, vitamin B9, which is indispensable for living organisms. Mammalians assume this
molecule in the diet, whereas bacteria produce it through a biosynthetic pathway which
utilizes p-aminobenzoic acid (Figure 26). The structure of sulfonamides mimics that of
p-aminobenzoic acid, the carboxylic acid being substituted by a very similar, but
ineffective functional group (the sulfonamide).
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7. Molecules of Life
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Living organisms generate and contain an enormous variety of organic compounds,
some of them are particularly relevant as structural and functional components, whereas
others are present in very small quantities and act as regulators, messengers, or defense
compounds. It is not easy to classify natural compounds depending on their role.
Carbohydrates, for example, perform structural roles like cellulose in plants or chitin in
the insect exoskeleton, roles of energy reserve like in starch, roles of cellular
recognition in cell wall glycoproteins and glycolipids. It is easier therefore to classify
natural compounds depending on their structure. The main classes of natural
compounds are: carbohydrates (glycides), amino acids and proteins (protides), nucleic
acids (nuclides) and lipids.
7.1. Carbohydrates
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Carbohydrates are a wide and important class of organic compounds, the most abundant
in Nature. It is well known that plants are able to generate glucose from water and
carbon dioxide in a process called photosynthesis which exploits the energy of the sun.
This is an example of generation of organic compounds from inorganic starting
materials. On the other hand, it is known that living organisms produce the energy they
need via the opposite process: glucose is converted into carbon dioxide and water with
liberation of energy. The two processes are very complex and their description requires
the knowledge of the reaction mechanisms, therefore they will not be discussed at this
level.
Carbohydrates are organic compounds characterized by the presence of a carbonyl
group (generally aldehyde or ketone) and multiple hydroxyl groups. Figure 27 shows
how many different sugars can exist depending on the number of carbon atoms and the
stereochemistry of each stereogenic centre. The sugars shown in Figure 27 are aldoses
(contain an aldehyde) with three, four, five and six carbon atoms— and all present the
last hydroxyl group to the right (D-series by definition). The mirror images of the sugar
shown in Figure 27 maintain the same name, but with the prefix L (L-series by
definition) instead of D.
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Figure 27: Aldoses with three, four, five and six carbon atoms, all presenting the last
hydroxyl group to the right (D-series)
The most relevant behavior of carbohydrates is their ability to generate a cycle by
reaction of the carbonyl group with a hydroxyl group of the same molecule, and the
capacity of the same carbon atom, called “anomeric centre”, to link another hydroxyl
group of a different molecule (Figure 28). This different molecule can be any type of
alcohol or some amino groups. Of particular interest is the case in which the alcohol
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belongs to another molecule of sugar; in this way oligosaccharides and polysaccharides
are formed. The process with which a sugar links another molecule, exploiting the
anomeric centre and the alcoholic function of the other molecule, is defined
glycosylation. In glycosylation two different stereoisomers can be generated the αanomer and the β-anomer (see Figure 28). The stereochemistry of this linkage is very
important and influences very much the properties of the two different compounds:
cellulose and starch differ only for the stereochemistry of the glycosidic linkage (Figure
29).
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Figure 28: Glucose generates a cyclic structure by reaction of the carbonyl group with
one of the hydroxyl group of the same molecule. This cyclic compound can link the
hydroxyl group of a second molecule ROH.
Figure 29: Cellulose and starch differ only for the stereochemistry of the glycosidic
linkage
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Carbohydrate chains, linked to proteins (glycoproteins) or lipids (glycolipids) decorate
the cell walls and participate in cellular recognition phenomena responsible for cell
adhesion, development, differentiation, morphogenesis, fertilization, immune response,
signaling and other cellular events including cancer metastasis. To give an example,
blood groups determinants A, B and H are constituted by a sugar sequence. In blood
group determinant H an L-fucose links with an α-anomeric configuration the hydroxyl
group in position two of D-galactose, which in turn links, with a β-anomeric
configuration, a molecule of N-acetyl-D-glucosamine. In the determinant of blood
group A, a further sugar, N-acetyl-D-galactosamine links position three of the Dgalactose unit of the trisaccharide of group H. In the determinant of blood group for
group B, D-galactose links position three of the D-galactose unit of the trisaccharide of
group H.
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Carbohydrates have primary importance in food. Sucrose (Figure 15), the table sugar, is
the main sweetener used in nutrition; this disaccharide is converted by the enzymes
present in saliva into glucose and fructose, also used as sweeteners. The disadvantage of
these sugars as sweeteners consists in the fact that they are caloric and favor dental
caries by microbial oxidation of the aldehydes which generate the corresponding
carboxylic acid. In order to avoid this problem, other sweet sugars lacking the aldehyde
group have been used in the food industry: mannitol, sorbitol and xylitol are examples
of widely used non carcinogenic sweeteners (Figure 30).
Figure 30: Monnitol, sorbitol and xylitol, three sugars used in the food industry as
sweeteners
Less caloric sweeteners such as saccharin, which is 300 times as sweet as sucrose, and
aspartame which is 200 times more sweet than sucrose, does not belong to the class of
sugars (Figure 31).
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Figure 31: Non caloric sweeteners.
Starch, ubiquitous in our diet (bread, rice, pasta, pizza, …) is also degraded
enzymatically into units of glucose which are used by the organism in glycolysis to get
energy.
7.2. Amino Acids, Peptides and Proteins
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Proteins are polymers constituted by the 20 different amino acids shown in Figure 32.
The amino acids are molecules that contain in the same structure an acid (the carboxylic
acid) and a base (the amino group), therefore they exist as internal salts (zwitterions).
All proteogenic (that generate proteins) amino acids are α-aminoacids, which means
that the amino group is on the carbon atom adjacent (in position α) with respect to the
carboxylic acid. Furthermore they are all chiral, except glycine, and the stereochemistry
is L according to the Fisher descriptor (see Section 3.3).
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Depending on the nature of the side chain, amino acids are divided into not polar, polar
and charged. The nature of the side chain is very important; as a matter of fact in
proteins the carboxylic and the amino groups are involved in the linkage that generates
the chain, whereas the side chains are responsible for the properties and functions.
Structural proteins such as collagen are poorly functionalized; they are made mainly
from glycine, which has no side chain. Functional proteins, such as enzymes, generate
globular structures containing cavities (the active site of the enzyme). Depending on the
size of the cavity, and the presence of non polar, polar or charged side chains in the
active site of the enzyme, specific molecules (the substrates of the enzyme) can
accommodate generating adequate attractive interactions, and undergoing the reaction
that the enzyme catalyses.
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Figure 32: The 20 amino acids that constitute the proteins
In living organisms amino acids are present not only in proteins; they also constitute
peptides that play relevant physiological roles. An example, is angiotensine II, an
octapeptide with potent vasoconstrictor activity.
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Amino acids are exploited by living organisms as starting materials to generate a variety
of other metabolites. For example, adrenaline, the “fight or fly” hormone, is generated
from the amino acid tyrosine (Figure 33).
Figure 33: The hormone adrenaline is generated from the amino acid tyrosine.
There is currently great interest in aminoacids as nutraceutics (in sports and health care),
and therefore industrial methods to synthesize them stereoselectively present industrial
interest.
7.3. Nucleic Acids
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Nucleic acids, RNA and DNA, are the organic compounds responsible for the
transmission of genetic information. They are polymers made by the sequence of
monomeric entities formed by three different parts: a sugar, a “base” and a phosphate.
The backbone of nucleic acids is essentially formed by the sugar, ribose in RNA and 2deoxyribose in DNA, linked to each other through a phosphate bridge (see Figure 34).
Each sugar links, at the anomeric centre, a so called “base”, that is an aromatic
compound containing some nitrogen atoms (therefore termed as heteroaromatic
compounds). Two bases, adenine (A) and guanine (G), contain two heteroaromatic
fused cycles derived from a so called purine skeleton; these bases are also called purine
bases. Two other bases, cytosine (C) and thymine (T) (uracil, U, in RNA) present a
structure containing only one heteroaromatic cycle, derived from the skeleton of
pyrimidine, which are therefore called pyrimidine bases.
The chemical structure of the bases is made so that a couple of them, a purine and a
pyrimidine, are “complementary”. Adenine is complementary to uracil in RNA or to
thymine in DNA (A-U or A-T), whereas guanine is complementary to cytosine (G-C).
This complementarity is due to the hydrogen bonds that can be generated between the
two complementary bases (Figure 35) and allows the generation of a complementary
filament of nucleic acid that is at the basis of the transmission of the genetic
information. The two complementary filaments of DNA generate a double helix
structure
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Figure 34: Nucleic acids, RNA and DNA
Figure 35: The complementarity of nucleic acid bases.
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The process by which DNA replicate themselves in the nucleus of cells is termed as
replication. Replication of DNA begins by partial unwinding of the double helix, and
the generation of a complementary chain. In each molecule of DNA therefore one chain
comes from the original filament whereas the other is enzymatically synthesized
choosing the complementary bases.
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RNA has a different role, it takes the information from DNA and utilizes this
information for the synthesis of proteins. This is a complex process, in which three
types of RNA are utilized, the messenger RNA ( m-RNA) that carries the genetic
information from DNA to the ribosomes, where the proteins are synthesized; the
ribosomial RNA (r-RNA) which generates ribosomes in combination with proteins; and
the transfer RNA (t-RNA) which is able to transport specific amino acids to ribosomes,
where they are joined together to generate proteins. Each of the 20 proteogenic amino
acids has at least one t-RNA molecule that carries it to the ribosomes.
Figure 36: Adenine and phophorylated derivatives
The monomers constitute nucleic acids— the base linked to ribose that is called
nucleoside (agenosine, guanosine, cytosine, uridine). The nucleoside phosphorylated in
position 5 is defined nucleoside phosphate (or nucleotide) (Figure 36).
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Figure 37: The enzymatic glycosylation process is an example of utilization of
nucleoside diphosphate derivatives, in the specific case reported in figure, UDPglucose.
Nucleosides and nucleoside phosphates are widely used in living organisms for roles
other than the formation of nucleic acids. ATP (adenosyl triphosphate) for example is a
molecule that furnishes energy in a good number of enzymatic processes. Nature
exploits nucleotide triphosphates taking advantage of the high reactivity of the
triphosphate group. One example of this utilization is the glycosylation process in which
a sugar links at the anomeric position the hydroxyl group of another sugar (or a different
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molecule such as serine in glycoprotein synthesis). Glucose, for example, reacts with
uridine triphosphate (UTP), to generate UDP-glucose and inorganic phosphate (Figure
37). UDP-Glucose reacts with the alcoholic function of another molecule with
formation of the glycoside and liberation of UDP.
7.4. Lipids
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Lipids are hydrophobic biomolecules soluble in organic solvents and insoluble in water,
displaying a wide range of biological functions in the cell. Lipids include a broad range
of natural products, like fatty acids and their derivatives, carotenoids, terpenoids,
steroids, bile acids. A most common type of lipid present in Nature is fatty acids. These
are long chain carboxylic acids, with an even number of carbon atoms, as shown in
Figure 7 for palmitic and oleic acid, Fatty acids are linked to glycerol, or to other
alcohols such as cholesterol via an ester linkage, or to sphingoid bases via an amide
bond. In addition they may contain alkyl moieties other than fatty acids, phosphoric
acids, organic bases, carbohydrates and other components.
Even if lipids cannot be grouped in terms of functional groups, they can be divided into
two main categories: hydrolysable lipids such as waxes, triglycerides, phospholipids
and glycolipids, and non-hydrolysable lipids such as terpenoids, steroids and some
vitamins.
Hydrolysable lipids are cleaved, by treatment with alkali, such as sodium hydroxide,
into two components, one of which is invariably the salt of a fatty acid, a carboxylic
acid with a long chain with an even number of carbon atoms. These salts constitute the
soaps, and the process, which is known from the old times, is defined saponification.
7.4.1. Fats, Oils and Waxes
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Triglycerides constitute the common fats and oils, and play the main role of energetic
reserves; they are formed by three fatty acids which esterify glycerine; an example is
represented in Figure 20. Besides triglycerides, a variety of diacylglycerols are present
in living organisms, the third hydroxyl group of which links a polar residue such as
phosphatidyl choline (in phospholipids) or a sugar (in glycolipids) (Figure 38). Waxes
are esters of fatty acids and long chain alcohols.
7.4.2. Phospholipids and Glycolipids
Phospholipids and glycolipids are assembled in a double layer, so that the hydrophobic
chain aggregates in the internal part, whereas the polar part is at the surfaces and
interacts with the aqueous medium inside and outside the cell. The lipophilic internal
part of the cell wall membrane plays a very important physiological role: polar
compounds, including ions, cannot penetrate into the cell indiscriminately, but require
specific mechanisms of transport.
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Figure 38; Hydrolysable lipids
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7.4.3. Terpenoids
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Terpenoids are a wide variety of organic compounds formed by repeating five-carbon
units called isoprene units (Figure 39). They can be linear, or cyclic, and can have
heteroatoms, especially oxygen, included in their structure (Figure 40). Many essential
oils isolated from plant sources by distillation, such as citral or cedral shown in Figure
40, are terpenoids.
Figure 39: The isoprene unit
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Figure 40: Terpenoids
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7.4.4. Fat-soluble Vitamins
Figure 41: Fat-soluble vitamins
Vitamins are organic compounds required in small quantities for normal metabolism,
and usually cannot be synthesized by our body and must be taken up with the diet.
Vitamins A, D, E and K are fat-soluble vitamins found in fruits and vegetables (Figure
41)
Vitamin A is synthesized from β-carotene; in the organism it is oxidized to 11-cisretinal (the corresponding aldehyde), the light sensitive compound responsible for
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vision in all vertebrates. It is also needed for healthy mucous membranes. A deficiency
of vitamin A causes night blindness, as well as dry eyes and skin.
Vitamin D3 is the most abundant of D vitamins; it can be synthesized by the body from
cholesterol. Vitamin D is involved in calcium and phosphorus metabolism. Deficiency
of vitamin D causes rickets, spinal curvature, and other deformities.
The term vitamin E refers to a family of structurally similar compounds, the most
biologically active being α-tocopherol (Figure 41). Vitamin E acts as antioxidant; a
deficiency of vitamin E causes numerous neurological problems.
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Vitamin K (phyllokinone) regulates the synthesis of proteins needed for blood clotting.
A deficiency of vitamin K leads to excessive and sometimes fatal bleeding.
7.4.5. Steroids
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Steroids are a class of organic compounds containing a common skeleton with four
condensed cycles.
Figure 42: Steroids
Cholesterol, the most abundant steroid in animal tissue, has an important role in
membranes and in lipid metabolism. Elevated cholesterol levels are associated with the
pathogenesis of the cardiovascular system. Many other important steroids are hormones
secreted by the endocrine glands, such as sex hormones (Figure 42). Estradiol and
estrone are estrogens synthesized in the ovaries; they control the development of
secondary sex characteristics in females and regulate the menstrual cycle. Testosterone
and androsterone are androgens synthesized in the testes; they control the development
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of secondary sex characteristics in males. Progesterone (pregnancy hormone) is
responsible for the preparation of the uterus for implantation of a fertilized egg.
8. Organic compounds in the market
The market of organic compounds has reached an impressive level; it ranges from
petroleum, currently the most abundant and economic source of starting materials for
the chemical industry, to structurally complex and expensive medicinal drugs. The
variety of organic compounds that find application and use explains the flourishing state
of the chemical industry in developed countries, which strongly contributes to their
economical growth.
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With regard to fossil reserves, we are now faced with the paradoxical situation that
while crude oil (petroleum) is being consumed faster than ever, the “proven oil
reserves” have remained at about the same level of thirty years ago as a consequence of
new oil findings. Nevertheless, these “proven oil reserves” are located in increasingly
difficult to reach places. Therefore, the cost of extracting crude oil rises continuously, as
reflected in increasing oil prices. Agricultural by-products such as straw are 10 times
less expensive than petroleum. The ability to use renewable materials is of utmost
importance and has significant growth perspectives. It can be speculated that 5 billion
tons of renewable materials could be used for the synthesis of approximately 1 billion
tons of organic products, fully meeting our need for chemicals.
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We can divide the chemical market into two main categories, that of bulky-chemicals,
low added value compounds produced in thousands of tons, and that of fine-chemicals,
high added value compounds in some cases produced in kilos or even in grams scale
(such as some vaccines for example). The methods of production, equipment and
environmental impact of a chemical factory are quite different depending on which
category of organic compounds it produces; developed countries tend to invest in the
production of fine-chemicals.
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8.1. Dyes
The origin of the chemical industry goes back to the beginning of the XX century in
Germany, when factories for the production of dyes from aniline were created. At that
time dyes were obtained from natural sources and some of them, like carminic acid
(Figure 43), the red pigment obtained from coccid insects, were very expensive.
Figure 43: Carminic acid.
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The reaction of aniline derivatives with sodium nitrite and hydrochloric acid affords a
reactive compound, defined diazonium salt, which is able to react with aromatic
compounds to generate a class of dies such as the “para red”, a cotton dye, or the butter
yellow that was used as food coloring for margarine before being considered
carcinogenic (Figure 44).
Figure 44: Synthetic dyes derived from aniline.
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In general, dyes are compounds with an extensive presence of double bonds alternated
with single bonds a characteristic, called conjugation that allows the absorption of light
at the wavelength of the visible light (400-750 nm). The presence of heteroatoms such
as oxygen, sulfur or nitrogen, modulates the color. Dyes are classified as natural dyes
and synthetic dyes. As far as the structure concerns, synthetic dies are generally made
from aromatic compounds, in order to take advantage of the extensive conjugation of
double bonds present in aromatic compounds, and are divided into a) dyes derived from
aniline, b) dyes derived from phenols, c) dyes derived from heteroaromatic compounds.
It is interesting to mention that from the dye industry, an important class of antibacterial
agents, the sulfonamides, was discovered. In 1913 it was serendipitously observed that
one dye derived from aniline, crisoidine (Figure 44), showed antibacterial activity.
Following this observation in 1927 at Farbenindustrie in Germany, a systematic study
was made on the antibacterial activity of this class of dyes, and in 1932 prontosyl
rubrum (Figure 44) a new dye with strong in vivo antibacterial activity was discovered.
However, prontosyl rubrum did not show any activity in vitro. Subsequent studies
indicated that the active molecule was the sulfonamide prontosyl album (Figure 45)
produced in the organism by degradation of prontosyl rubrum. Prontosyl rubrum is
therefore a pro-drug (a molecule that will generate a drug), whereas the real drug is
prontosyl album. This example is an interesting case in which a discovery starts from an
observation and proceeds with a clever and deliberate research. From this discovery a
pharmaceutical industry had originated.
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Figure 45: Prontosyl album, a sulfonamide.
Figure 46: Some dyes approved by the FDA for use in food.
The pharmacological properties revealed by same dyes suggest that some of them could
be dangerous for our health. Some dyes revealed in fact carcinogenic properties. The
nature and chemical properties of the dye of choice depend on what must be colored:
tissues, walls, plastics, paper and even food and beverages. Particular attention is
actually devoted to the safety of dyes, in particular if they are used as additives in food
and beverages or for food packaging. Some safe dyes, approved by the Food and Drug
Administration (FDA) for use in food and ingested drugs, are shown in Figure 46.
An interesting example of a safe dye of natural origin is astaxanthin, a pink pigment
with a terpenoid structure that is used, inter alia, to feed sea-farm raised salmon to
obtain the beautiful pink salmon meat. Wild salmons get the pigment from their natural
diet.
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8.2. Compounds for Health Care
The main classes of organic compounds used for health care are medicinal drugs,
nutraceutics and cosmetics. The market of these compounds is very florid, and the
added value in their production is particularly high.
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Medicinal drugs are the most important compounds for health care. From the use of
herb extracts as medicaments, and the isolation of their active principles, medicinal
chemistry has grown as a mature science that is able to understand the molecular
mechanisms of many pathological phenomena and to design in a rational way new
medicinal drugs. On the other hand, the cost of pharmaceutical research, from the
design and synthesis of a new drug to the approval for medicinal use, is becoming more
and more expensive, due to the increasing costs of the pharmacological studies required
to certify the safety of the new compound.
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Antibiotics and their intermediates are among the most important fine chemicals, with a
world market value of about 20 billion euro. Most antibiotics, such as penicillin,
cephalosporin and tetracycline are products of the secondary metabolism of
microorganisms, and therefore they are almost exclusively made by fermentation
processes .The structural complexity of most antibiotics, such as tetracycline or
streptomycin (Figure 47), is so great that chemical synthesis is problematic. Only in the
case of so-called semi-synthetic antibiotics, the building blocks are obtained by
fermentation, and subsequently chemically modifications generate new antibiotic
derivatives with improved effectiveness. This is the case of penicillin (Figure 47),
penicillin G is obtained by fermentation, whereas amoxicillin is a semi-synthetic drug.
Figure 47: Structure of some antibacterial agents.
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There are also examples of totally synthetic drugs, such as sulfonamides, as seen before,
or benzodiazepines such as Valium (Figure 48), a widely used tranquillizer, obtained by
systematic screening made on a wide variety of synthetic organic compounds.
Figure 48: Structure of Valium (Diazepam), a benzodiazepine
The theme of medicinal chemistry is described in Chemistry of Nutraceutics, Flavors,
Dyes and Additives. Humanity has taken great advantage from the discoveries of
medicinal chemistries, and many diseases have been defeated.
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Nutraceutics refers to compounds, such as vitamins, amino acids and other tonics and
energizing substances that contribute to our health. The use of nutraceutics, as additives
in food and beverages, or in pills for use in sports, is increasing mainly in developed
countries not only among athletes but also in the public at large.
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Amino acids are increasingly used as supplements in human food and animal feed. The
world-wide production of L-glutamic acid, for example, is over 1 million tons a year. It
is one of the most important fermentation products with a tonnage comparable to many
petrochemical products. Glutamic acid is used in the form of monosodium glutamate as
a taste enhancer in many foods. L-lysine (350,000 t/year) is another large-scale
produced amino acid, mainly used in animal feed. L-Phenylalanine is yet another amino
acid, taking part in the synthesis of L-aspartame. L-Carnitin (Figure 49) is a vitaminlike natural component in animal tissues that stimulates lipid metabolism. Initially, Lcarnitine was produced via chemical synthesis, but is now entirely made through a
fermentation process, starting from renewable raw materials. The L-carnitine obtained
in this way is very pure and is increasingly used as a food supplement for humans and
animals since it stimulates their fat metabolism (more energy, reduced fat synthesis and
increased growth).
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Figure 49: Carnitine, essential cofactor for fatty acid metabolism
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Vitamins are important fine chemicals that are produced in relatively large quantities.
Whereas a number of vitamins can be prepared only via biotechnology such as vitamin
B12, other more simple vitamins can be produced by either a chemical route or a
biotechnological route and quite often by a combination of both. The synthesis of
vitamin B2 (riboflavin, 4,000 t/year) is a good example of this. The conventional
process consisted in the synthesis of the building block D-ribose by fermentation with
Bacillus bacteria, followed by a sequence of chemical reactions to obtain riboflavin.
8.3. Compounds for Food Industry
Sweeteners, flavors, colorants, emulsifiers and preservatives are the main class of
organic compounds that have found application in the food industry.
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The most important sweetener is sucrose, a sugar (disaccharide) known as table sugar.
The limits of sucrose lie in its caloric content and induction of dental caries. Some sugar
alcohols, such as sorbitol, xyliton and mannitol (Figure 50) are used in food industries
as sweeteners that do not contribute to the formation of caries. Dietetic sweeteners are
those compounds that, being some order of magnitude sweeter than sucrose, are used in
quite small amounts. Moreover, some of them cannot be metabolized and therefore are
not caloric.
Aspartame (Figure 50) is an artificial sweetener 200 times sweeter than sugar. It is used
in many foodstuffs, such as “light” beverages. Worldwide, around 15,000 tons of
aspartame are produced each year at an approximate world market price of 35 €/kg.
Saccharin (Figure 50) is 300 times sweeter than sucrose; it does not contribute energy or
calories. Saccharin has been the centre of controversy for many years because of its
alleged relationship with cancer; however, research studies have been unable to
find direct associations. Cyclamate is 30 times sweeter than sucrose; is heat stable, and
so can be used in hot and cold foods.
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Figure 50: Some common sweeteners
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Flavors are more or less volatile substances produced by fruit or vegetables during
different stages of ripening or during manipulation. In particular ripening is the main
process through which fruit flavors are produced, while manipulation (like cutting or
chewing) is the main cause of vegetable flavor generation. Natural flavors are generally
due to a mixture of volatile organic compounds, and the difficult task is to mix them in
an appropriate manner. Vanillin, the fragrance of vanilla; cinnamyl aldehyde, the
fragrance of cinnamon; 4-Decalactone, a peach aroma; α-ionone, responsible for the
flavor of violet, are just some examples of fragrances that find industrial application
(Figure 51).
Figure 51: Some common flavors
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Food manufacturers add preservatives to the food preparation, which prevent spoilage.
Preservatives serve as either antimicrobials or antioxidants or both. As antimicrobials,
they prevent the growth of molds, yeasts and bacteria. As antioxidants, they keep foods
from becoming rancid, browning, or developing black spots. Antioxidants suppress the
reaction that occurs when foods combine with oxygen in the presence of light, heat, and
some metals. Antioxidants also minimize the damage to some essential amino acids, the
building blocks of proteins, and the loss of some vitamins.
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Antioxidant can be classified in two main classes according to their specific action:
primary and secondary antioxidants. Primary antioxidants are compounds that interrupt
the free-radical chain of oxidative reactions, themselves forming stable free radicals
which do not initiate or propagate further oxidation of lipids. Some primary antioxidants
are substituted phenols obtained by synthesis, such as butylated hydroxyanisole (BHA)
or alkyl gallates, or of natural origin, such as tocopherols (Figure 52).
Figure 52: Examples of primary antioxidants
Secondary antioxidants can also retard rancidity by different mechanisms. They can be
reducing agents or "oxygen scavengers" or chelating agents. Ascorbic acid, citric acid,
and ethylenediaminetetraacetic (EDTA) belong to this second class (Figure 53).
Ascorbic acid functions as an oxygen scavenger, making it particularly useful in canned
or bottled products with a headspace of air.
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Figure 53: Examples of secondary antioxidants
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Antimicrobial preservatives prevent the growth of molds, yeasts and bacteria. Among
the most diffused antimicrobial agents there are benzoic acid and its esters, esters of phydroxybenzoic acid, sorbates, sulfur dioxide, nitrites and nitrates (Figure 54).
Figure 54: Examples of antimicrobial preservatives.
Many food systems are composed of two incompatible substances: water (hydrophilic,
polar) and oil (lipophilic, non-polar). Since oil and water are unmixable, they require
mechanical agitation for dispersion. However, the contact between fat and water is
energetically unfavorable, such dispersions are thermodynamically unstable. It is
therefore necessary to incorporate emulsifiers and stabilizers in food emulsions to
extend shelf life. Some common food emulsions are cream, butter, margarine,
mayonnaise, salad dressing, sausage, ice cream, chocolate, milk, egg yolk and many
others.
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Emulsifiers can be divided into two categories: small molecules such as mono- and
diglycerides, sucrose esters, sorbitan esters (SPAN), polysorbates (TWEEN), stearoyl
lactylates, lecithin and derivatives (Figure 55), and macromolecules such as proteins
like bovine serum albumin, beta-lactoglobulin, lysozyme, and ovalbumin
Figure 55: Some common small molecular weight emulsifiers.
An emulsion system can be stabilized by increasing the viscosity of the continuous
phase. Gelatin and gums are not surface active at the interface; however, they are useful
in stabilizing oil/water emulsions because of their effect on the viscosity of the aqueous
phase.
8.4. Polymers
Polymers (from the Greek words “poly” = many, and “meroi” = units) are long-chain
molecules constituted by numerous repeating units of monomers linked together.
Polymers can be either natural, like cellulose, DNA, proteins, or synthetic, like
polystyrene. Both classes are relevant in our life and strongly contribute to our
commodities. Fibers, such as cotton, silk, polyester fibers; plastic materials made by
polyethylene, polystyrene; gums and resins have daily application.
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A large group of polymers behave as plastic materials. Every year around 100 billion
tons of diverse plastics are currently produced in the world. The reasons for this
commercial success are the low cost of precursors and simple processing, combined
with good properties, such as low density, resistance to corrosion and mechanical
strength. Several commodities for different applications are currently made of plastics
such as any sort of packaging, shoppers, bottles for soft drinks, synthetic fibers, toys,
car components, and furniture components and so on. Polymers are used also for
advanced applications, such as biodegradable and biocompatible materials for surgery
or for tissue regeneration, or techno-polymers with improved thermal and mechanical
resistance for the aerospace industry and for any other advanced application, including
sport. The largest use of plastics is in packaging, which account for about 30 percent of
the annual plastics production. About 15 percent of plastics are used for heavy-duty
building materials, and another 14 percent for consumer products. Other plastics are
used in transportation products, furniture, agriculture, and various biomedical
applications.
Almost all plastics are made from oil or natural gas, which are presently the cheapest
starting material. These sources however are non-renewable, and although plastics only
account for six to eight percent of the total oil and gas consumption, this fraction looks
significant in view of environmental considerations. Despite the size and efficiency of
the world’s oil industry makes it the cheapest starting material for the production of
organic compounds, research efforts are made in order to generate plastics from
renewable sources.
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The production of plastics from renewable sources can be achieved by identifying
sources of abundant polymers in Nature, or by producing monomers through bacterial
fermentation or chemical modification of natural compounds, in particular
carbohydrates. Typical polyesters that can be made from renewable resources are
poly(glycolic acid) (PGA) and poly(lactic acid) (PLA), whose monomers are produced
by fermentation. PLA is a rigid material which finds applications for thermoformed
products such as containers, drink cups and so on.
Most plastics have been engineered for being durable, despite most people use them
once or a few times and then throw away. Durable plastics are persistent in the
environment; therefore improperly disposed plastic materials are a significant source of
environmental pollution. Recycling of conventional plastics is in principle a way of
reducing the problems associated with plastic waste. De-polymerization technologies
have also been developed that can return the plastics to their starting reagents.
Incineration has the advantage that the plastics have high caloric values, but gas
emissions must be taken under control to ensure that no toxic gases are released.
Biodegradable plastics are particularly welcome for the production of disposable
materials. Traditional candidates for biodegradable polymers are represented by
polysaccharides, as for instance starch and cellulose grafted and blended to improve
processability and physical properties. Poly(glycolic acid) (PGA) and poly(lactic acid)
(PLA) are biodegradable and, as mentioned before, the monomers are produced by
fermentation.
©Encyclopedia of Life Support Systems (EOLSS)
ORGANIC AND BIOMOLECULAR CHEMISRTY – Organic and Bio-Molecular Chemistry - Francesco Nicotra
Some biodegradable polymers can be generated by bacterial species from simple
metabolic intermediates. This is the case of some polymeric materials collectively
known as poly-hydroxyalkanoates (PHA). Naturally produced biodegradable polyesters
are represented by poly-hydroxybutyrate-co-polyhydroxyhexanoates (PHBHs)
copolymers, completely biodegradable under aerobic as well as anaerobic conditions,
and are digestible in hot water under alkaline conditions.
9. Isolation, Purification and Analysis of Organic Compounds
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At the origin of organic chemistry the isolation, purification and determination of the
structure of natural organic compounds fascinated numerous scientists, and required
experimental ability, intelligence and fantasy. At that time the methods for the isolation
of a single compound from a complex mixture were few and relatively naïf: extraction
and partition between two immiscible solvents, usually water and chloroform or ethyl
ether, and crystallization. Exploiting these procedures, and in particular taking
advantage from the ionizable functional groups, carboxylic acids and amino groups, a
variety of natural compounds have been isolated. The term alkaloids, for example,
refers to a class of lipophilic natural compounds containing an amino group. These
compounds can be isolated from the natural sources by extraction of all the lipophilic
molecules with an organic solvent, then acidification, in order to convert the amino
group of alkaloids into the corresponding ammonium salt, and extraction of the organic
phase with water, in which the ammonium salt is soluble. Subsequent treatment of the
aqueous phase with a base converts the ammonium salt into the corresponding amine,
which is no more soluble is water and separates as solid precipitate or alternatively can
be extracted with an organic solvent. A great variety of bioactive organic compounds,
belonging to the class of alkaloids, such as cocaine, nicotine, adrenaline, morphine,
stricnine, have been isolated from plant extracts exploiting this procedure.
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At the beginning of the XX century a new powerful separation technique was
discovered: chromatography. In a paper published in 1906 Mikhail Tswett reported the
separation of pigments of vegetal origin, among which chlorophyll, by filtration of the
extract in petroleum ether on a column containing calcium carbonate. These results
stimulated subsequent studies, that allowed us to develop different and very
sophisticated chromatographic methodologies, which are all based on the “competition”
between a stationary phase (in the first example sodium carbonate), and a mobile phase
(in the first example petroleum ether) in the attractive interaction with the different
compounds in the mixture. Compounds with higher affinity with the mobile phase will
be transported faster through the stationary phase and vice versa. A great variety of
different stationary and mobile phases, based on different type of interactions
(adsorption, repartition, ionic, affinity, ..) have been developed, and nowadays
chromatography is the most powerful method for separation and analysis of organic
compounds.
Once a single compound has been isolated, it is important to determine its structure.
Chemists have two possibilities for structure determination: comparison with known
compounds or ex novo determination. If the compound is already known, the
comparison with an authentic sample could be enough. As with the finger print, this
comparison is based on the identity of an adequate number of physico-chemical
©Encyclopedia of Life Support Systems (EOLSS)
ORGANIC AND BIOMOLECULAR CHEMISRTY – Organic and Bio-Molecular Chemistry - Francesco Nicotra
properties, such as boiling or melting points, chromatographic behavior and the spectra
of adsorption of Infra Red light. With new instrumental techniques there is also the
possibility of gaining structural information. Mass spectroscopy (MS) permits us to
know the molecular weight of the compound and other structural information based on
the usual and classified fragmentation patterns of organic compounds in the
experimental conditions adopted. Nuclear Magnetic Resonances (NMR) affords precise
information on the arrangement of hydrogen, carbon, nitrogen and phosphorous atoms
in the organic molecule, that allow us to get the structure. X-rays provide a sort of
“photo” that shows the arrangement of atoms in the molecule.
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Presently, the structure of even very complex organic molecules, such as some proteins,
can be determined exploiting sophisticated instrumental analysis, and the presence of
even small traces of undesired organic compounds in air, food and beverages can be
detected. Accurate chemical analysis of the components allows us also to certify the
origin of food and beverages, and detect adulterations, in other words furnish a robust
contribution to the safety of our environment and alimentation.
10. Conclusions
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Organic and Bio-Molecular Chemistry contributes in so many ways to our healthy life
and to our commodities, that in this short chapter it has been possible to mention just
some of them. Most of the tools we use every day, such as the wheel of our car or the
small bags in which the greengrocer put our fruit, comes from the polymerization
technology that exploits organic compounds. The soap, the creams, the cosmetics, and
much more important the medicinal drugs that we use for our health care, are all results
of the organic chemistry research. There results have been obtained thanks to the results
of the studies on the structure, the reactivity, the isolation and structural determination
techniques that have been developed by the Organic Chemists since the 19th century.
The progresses in this field will continue with the finding of new drugs, new materials,
and new commodities.
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In this Encyclopedia the theme of Organic and Bio-Molecular Chemistry has been
divided in 13 topics: 1) Organic Substances and Structures, Nomenclature of Organic
Compounds, 2) Stereochemistry, 3) Organic Chemical Reactions, 4) Synthetic Organic
Chemistry, 5) Organic Chemistry and Biological Systems –Biochemistry, 6) Chemistry
of Natural Compounds, 7) Medicinal Chemistry, 8) Chemistry of Nutraceutics, Flavors,
Dyes and Additives, 9) Computational Organic Chemistry, 10) Photochemistry, 11)
Organo-metallic Chemistry, 12) Polymer Chemistry and Environmentally Degradable
Polymers, 13) Organic Spectroscopy. The idea is to start with the structural aspects,
then move to the reactivity and the synthesis, describe the relevant categories of organic
compounds that find application, and finally discuss some methods of analysis. This
choice of course is personal and certainly not exhaustive, but allow us to understand
what Organic Chemistry is and what the potentialities of this science are.
Glossary
Activation
energy:
the minimum amount of energy required for a molecule to
perform a specific reaction
©Encyclopedia of Life Support Systems (EOLSS)
ORGANIC AND BIOMOLECULAR CHEMISRTY – Organic and Bio-Molecular Chemistry - Francesco Nicotra
naturally occurring amines of vegetal origin
organic compounds containing an amino and a carboxylic group,
20 of them constitute the proteins
organic compounds presenting a special stability due to the
Aromatic
circular delocalization of defined number of electrons.
compounds:
defined also sugars or glycides, are a wide class of compounds
Carbohydrates:
present in living organisms.
is a phenomenon that accelerates a reaction.
Catalysis:
is a chemical species responsible for the catalysis, therefore
Catalyst:
accelerating a reaction.
is a geometrical property that prevents us to superimpose an object
Chirality:
to its mirror image.
Chromatography: is an important method for separation of organic compounds based
on the competition of the attractive interaction of the compounds
to be separated between a stationary and a mobile phase.
Different possible spatial arrangement of the atoms of a molecule.
Conformations:
a measure of the charge separation in a molecule
Dipole moment:
a covalent bond formed by the shearing of two couple of electrons
Double bond:
between adjacent atoms; is made by a σ-bond and a π-bond
Electronegativity: The intrinsic ability of a chemical element to attract electrons.
A protein that act as catalyst in the organism
Enzyme:
refers to an organic compound used as additive in food to maintain
Emulsifier:
an emulsion and therefore preventing the separation of
hydrophobic compounds from the aqueous phase.
a chemical reaction that allow to link a carboxylic acid and an
Esterification:
alcohol generating an ester.
a class of natural compounds made by carboxylic acids with a
Fatty acids:
linear chain with an even number of carbon atoms.
Fisher projection a conventional method invented by Emil Fisher to describe the
stereochemistry of chiral molecules, in particular sugars and
formulas:
amino acids.
Functional group: the group of atoms and the associated bonds that define the
chemical behavior of a family of organic compounds.
aromatic compounds presenting one or more heteroatoms in the
Heteroaromatic
cyclic structure responsible for the aromaticity.
compounds:
in organic chemistry refers to all atoms except carbon and
Heteroatoms:
hydrogen.
the different combination of atomic orbitals obtained by
Hybridisation:
mathematical combination of the ground state atomic orbitals.
organic compounds containing only carbon and hydrogen atoms.
Hydrocarbons:
the bond between a hydrogen atom linked to an heteroatom and a
Hydrogen bond:
second heteroatom.
a term given to compounds that perform attractive interactions
Hydrophilic:
with water, and therefore are water soluble.
a term given to compounds that perform repulsive interactions
Hydrophobic:
with water, and therefore are not water soluble.
a compound that inactivate a catalyst, such as an enzyme,
Inhibitor:
therefore lowering the reaction rate.
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Alkaloids:
Amino acids:
©Encyclopedia of Life Support Systems (EOLSS)
ORGANIC AND BIOMOLECULAR CHEMISRTY – Organic and Bio-Molecular Chemistry - Francesco Nicotra
Kinetic of the
reaction:
Lipids:
London forces:
Monovalent:
Nucleic acids:
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Nucleoside:
studies the parameters that determine the speed of a chemical
reaction.
a class of natural compounds with the common feature to be
hydrophobic.
instantaneous molecular dipole moments due to a induced
asymmetric distribution of electrons in a molecule.
that can establish only one linkage.
biomolecules formed by the sequence of nucleosides, a
phosphorylated sugar (ribose in RNA and deoxyribore in DNA)
bonded to the purine or pyrimidine base, the sequence is generated
via a phosphate bridge that links a sugar to the subsequent one.
the portion of a nucleic acid that contains the sugar (ribose or
deoxyribose), bonded to the purine or pyrimidine base.
the portion of a nucleic acid that contains the phosphorylated
sugar (ribose or deoxyribose), bonded to the purine or pyrimidine
base.
compounds that find application in alimentation for health care,
such as vitamins, amino acids, etc.
high molecular weight compounds made of repeating units of
small molecules, defined monomers.
natural occurring polymers made by a sequence of amino acids.
refers to the 20 amino acids that constitute the proteins.
Nucleotide:
Nutraceutics:
Polymers:
Protein:
Proteogenic
amino acid:
Purine bases:
Pyrimidine bases:
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Saponification:
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Single bond:
Stereogenic:
Stereoisomers:
Steroids:
Terpenes:
Tetravalent:
Thermodynamic
of a reaction:
Transition state:
heteroaromatic bicyclic compounds, namely adenine and guanine,
present in nucleic acids.
heteroaromatic compounds, namely cytosine, thymine and uracil,
present in nucleic acids.
the hydrolysis of esters in basic conditions, which generates salts
of carboxylic acids (soaps in the case of long chain carboxylic
acids)
a covalent bond formed by the shearing of one couple of electrons
between adjacent atoms; is made by a σ-bond
refers to an atom bearing a number of different substituents (4 for
the carbon atom) so that the interchange of two of them generate a
different (non super-imposable) molecule.
refers to molecules that differ only for the arrangement of the
atoms or groups in the space.
a class of natural compounds containing a common skeleton with
four condensed cycles, that perform important biological
activities.
a class of natural compounds that originate biosynthetically by
junction of isoprene units, a chemical entity with 5 carbon atoms.
refers to an element that establishes four bonds, this is the case of
the carbon atom.
studies the energy parameters associated to a chemical reaction.
The point of maximum energy between reactants and products in a
reaction.
©Encyclopedia of Life Support Systems (EOLSS)
ORGANIC AND BIOMOLECULAR CHEMISRTY – Organic and Bio-Molecular Chemistry - Francesco Nicotra
Triglycerides:
Triple bond:
Vitamins:
Zwitterion:
a class of natural compounds, belonging to the so defined fats, that
are made by three units of fatty acid linked to a molecule of
glycerine.
a covalent bond formed by the shearing of three couple of
electrons between adjacent atoms; is made by a σ-bond and two πbond
organic compounds required in small quantities for normal
metabolism, and usually cannot be synthesised by our body and
must be taken up with the diet.
a molecule presenting a positive and a negative charge.
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Bibliography
The bibliography on Organic Chemistry is extremely wide, and most of the textbook are clear and
exhaustive. Some books with different characteristics are reported as examples.
Gorzynski Smith J. (2006) Organic Chemistry, McGraw-Hill International edition, New York [a modern
textbook that put into evidence the applications of organic compounds]
Schmid G. H. (1996) Organic Chemistry, Mosby-Year Book, Inc, St. Louis [an exhaustive didactic
textbook of organic chemistry]
Bruice P. Y., (2004) Organic Chemistry 4th Edition, Pearson Education, Inc. [an exhaustive didactic
textbook of organic chemistry]
Atkins R. C., Carey F. A. (2002) Organic Chemistry, a brief course, third edition, McGraw-Hill. New
York. [a concise didactic textbook of Organic Chemistry]
Solomons T. W. G., (2005) Organic Chemistry 8th Edition Custom with Student Study Guide 8th, Wiley,
New York [a widely appreciated textbook of Organic Chemistry]
Brown W. H. (1999) Introduction to Organic Chemistry: 2nd Edition. Wiley, New York [this
introductory book emphasizes the interrelation between organic chemistry and the biological and health]
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Clayden J., Greeves N., Warren S., Wothers P. (2001) Organic Chemistry. Oxford University Press [a
concise introductory textbook of organic chemistry]
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Biographical Sketch
Francesco Nicotra was born in Catania in 1950. He graduated in Chemistry at the University of Catania
in 1973; then he moved to the University of Milano where he became permanent researcher in 1981 and
associated professor in 1987. In 1985 he spent a post-doc period at the University of Orleans, under the
supervision of Pierre Sinay. Actually he is full professor of organic chemistry at the University of Milano
Bicocca and Director of the Department of Biotechnology and Biosciences. He is member of the IUPAC
Committee of Organic and Biomolecular Chemistry and chairman of the subcommittee of Biotechnology.
He is also the Italian representative in the International Carbohydrate Organisation. The research interests
ranges across the synthesis of various biologically active compounds, in particular carbohydrates and
structural analogs, the development of new synthetic methods and the use of biocatalysis.
To cite this chapter
Francesco Nicotra, (2003), ORGANIC AND BIO-MOLECULAR CHEMISTRY, in Organic and
Biomolecular Chemistry, [Ed. Francesco Nicotra], in Encyclopedia of Life Support Systems (EOLSS),
Developed under the Auspices of the UNESCO, Eolss Publishers, Oxford ,UK, [http://www.eolss.net]
©Encyclopedia of Life Support Systems (EOLSS)