Republic of the Philippines

CENTRAL BICOL STATE UNIVERSITY OF AGRICULTURE

San Jose, Pili, Camarines Sur 4418
Website: www.cbsua.edu.ph
Email Address: op@cbsua.edu.ph
Trunkline: (054) 871-5531-33 local 101

COLLEGE OF DEVELOPMENT EDUCATION

Learning Module in
WEEK
2 CHEM 102
Organic Chemistry

This learning module belongs to:

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This learning module is prepared by:

LUDIVICO B. HOMILLANO, EdD

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 Republic of the Philippines
CENTRAL BICOL STATE UNIVERSITY OF AGRICULTURE
San Jose, Pili, Camarines Sur 4418
Website: www.cbsua.edu.ph
Email Address: op@cbsua.edu.ph
Trunkline: (054) 871-5531-33 local 101

WEEK Nature and Structure of Organic

2 Compounds

EXPLORE

1.0 THE NATURE OF ORGANIC COMPOUNDS

Kekulé (Germany) and Couper (Scotland) were the first to recognize that
carbon is tetravalent - it can form four bonds, not only with other atoms (mainly H, O,
N) but also with other carbon atoms. The most distinctive feature of carbon atoms is
their capacity to form very' strong covalent bonds with each other. No other element,
including silicon, can do this. Silicon-oxygen-silicon bonds are easily cleaved. Silicon-
oxygen-silicon bonds are quite strong but do not result in the incredible diversity found
in carbon compounds.
Carbon atoms can link with each other to form linear, branched or cyclic
backbones for a wide variety of organic molecules. Take for example only four carbon
atoms and see the number of ways by which they can be linked to one another.

C C C

C C C
C ---- C ----- C
C ---- C ----- C ----- C C C
C

Linear /Unbranched Branched Cyclic

You can just imagine how many more diverse molecular frameworks can result
if there are more carbon atoms that are being linked to one another! Moreover, carbon
atoms may participate in single, double or triple bonds.
C C C C
C N C N C C
C O C O C N

single bond double bond triple bond

Page 2 of 15
 Republic of the Philippines
CENTRAL BICOL STATE UNIVERSITY OF AGRICULTURE
San Jose, Pili, Camarines Sur 4418
Website: www.cbsua.edu.ph
Email Address: op@cbsua.edu.ph
Trunkline: (054) 871-5531-33 local 101

The ability of carbon to form single as well as multiple bonds, not only with
another carbon atom, but also with atoms like nitrogen and oxygen, results in greater
diversity of molecular frameworks which constitute the skeletons of small and simple
molecules or big and complex biochemicals found in living organisms.
Organic molecules exhibit isomerism, a term derived from the Latin iso (equal)
and mer (part). There are two general types of isomerism: structural isomerism and
stereoisomerism. Structural isomers have the same molecular formula but structural
formulas, i.e. the same atoms can be put together in different ways resulting in
different compounds with entirely different properties. For example, two structural
formulas can be derived from the molecular formula C2H60, and each one
corresponds to a different compound.

ethyl alcohol dimethyl ether

liquid, bp 78.5 o C gas, bp-23.7 oC

As the number of carbon atoms increases, the number of possible structures

corresponding to a molecular formula also increases. If you take a look into Chemical
Abstracts, where known organic compounds are catalogued, you will see that there
are dozens and sometimes hundreds of different compounds that have the same
molecular formula.
The four bonds to carbon are directed to the four corners of a regular
tetrahedron. As a direct consequence of this, many different three-dimensional
structures can arise in organic molecules. This brings us to stereoisomerism (derived
from the Greek stereos - solid) - a more subtle kind of isomerism which is particularly
important in compounds found in living organisms. Stereoisomers have the same
molecular and structural formulas but differ from each other in their three-dimensional
structures.
Take the case of the amino acid alanine, whose structural formula is given below:

H3C— C— COOH

NH2
alanine

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 Republic of the Philippines
CENTRAL BICOL STATE UNIVERSITY OF AGRICULTURE
San Jose, Pili, Camarines Sur 4418
Website: www.cbsua.edu.ph
Email Address: op@cbsua.edu.ph
Trunkline: (054) 871-5531-33 local 101

Alanine can have two different three-dimensional structures which are mirror
images of each other.

CH3 CH3

COOH HOOC

H2N NH2
L - alanine D - alanine

The two different three-dimensional structures of alanine are related to one

another in the same way that our right and left hands are related, thus one is called
D - alanine (a right-handed molecule) and the other, L - alanine (a lefthanded
molecule). Like alanine, most of the molecules that make up plants and animals
exhibit handedness. Again, this phenomenon contributes greatly to the existence of
a tremendous number of organic compounds.
At this point you have probably realized that carbon is indeed very versatile
and why it is so. It should now be easy to understand why there are so many organic
compounds - much more than the combined compounds of the rest of the elements
in the periodic table.

So far, we have discussed the common features of organic compounds in

terms of their structures. Let us now go to the common behavior of organic
compounds as noted in the laboratory.

In general, organic compounds, which are largely covalent compounds, have

low melting points and limited solubility in water. Some are gases and many are
liquids at room temperature; those that are solids melt below 400 oC. In contrast many
inorganic salts, which are ionic compounds, melt above 1000 oC and dissolve
readily in water.
In addition to the above physical properties, organic compounds are generally
combustible (flammable) and/or are sensitive to heat (decomposed by heat). We
observe these properties in everyday life. Hydrocarbons are burned in order to
generate heat for cooking and to power motor vehicles. Table sugar (sucrose) is an
organic compound which is not combustible but is particularly sensitive to heat. In
caramelizing sugar for your leche flan, if you do not carefully control the fire, the sugar

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 Republic of the Philippines
CENTRAL BICOL STATE UNIVERSITY OF AGRICULTURE
San Jose, Pili, Camarines Sur 4418
Website: www.cbsua.edu.ph
Email Address: op@cbsua.edu.ph
Trunkline: (054) 871-5531-33 local 101

immediately decomposes extensively and is turned to carbon. Before going any

further, try to gauge what you have learned by doing the following exercises.

Organic chemistry is an empirical science whose development has depended

on millions of separate laboratory observations. These observations have been
rationalized and unified by the structural theory, the basis of which was laid down
between 1858 and 1861 by August Kekulé (Germany), Archibald Scott Couper
(Scotland) and Alexander M. Butlerov (Russia). This theory uses a few simple ideas
to account for diverse complex phenomena and to allow predictions to be made about
millions of compounds that have never been, but might be known. With the structural
theory as a guide, many organic chemists have designed and synthesized hundreds
of new organic compounds during their lifetimes.
Fundamental to the structural theory are two central premises:
1. Atoms in organic molecules form a fixed number of bonds; the measure of
this ability is called valence. For example, carbon forms four bonds and is
called tetravalent.
2. A carbon atom uses one or more of its valences to form bonds to other
carbon atoms, i.e., carbon can participate in single, double and triple
bonds.

We have used these concepts in the previous section to explain the diversity
of organic compounds. The following section will discuss the "HOW" and "WHY" of
these concepts, so that you can account for and make predictions about molecular
structures. Only a few of the millions of organic compounds already known will be
described in this course; however, you should be able to cope with others that are
not included because the fundamental principles governing these molecules will be
familiar.

2.0 ELECTRONIC STRUCTURE AND BONDING

You are already familiar with the fundamentals of the electronic structure of atoms.
The electrons in the outermost shell of an element are the ones involved in the
formation of chemical bonds and in chemical reactions. These electrons are called
valence electrons, and the energy level in which they are found is called the valence
shell. To show the outermost shell electrons of an atom, a representation called a
Lewis structure is used. In Lewis structures, the atomic symbol represents the
nucleus and all completely filled inner shells. The symbol is surrounded by a number
of dots equal to the number of valence electrons.

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 Republic of the Philippines
CENTRAL BICOL STATE UNIVERSITY OF AGRICULTURE
San Jose, Pili, Camarines Sur 4418
Website: www.cbsua.edu.ph
Email Address: op@cbsua.edu.ph
Trunkline: (054) 871-5531-33 local 101

2.1 THE FORMATION OF CHEMICAL BONDS

Gilbert N. Lewis pointed out that the chemical inertness of the noble gases
indicated a high degree of stability of the electron configuration of these elements (the
noble gases have completely filled valence shells). Lewis then devised a model of
bonding that unified many of the observations about chemical reactions of the
elements.
According to the Lewis scheme, atoms bond together in such a way that each
atom participating in a chemical bond acquires a completed valence shell electronic
configuration resembling that of the noble gas nearest it in the periodic table.
There are two ways by which atoms acquire completely filled valence shells:
1) gaining or losing enough electrons - an atom that gains electrons
becomes a negatively charged ion; on the other hand, an atom that loses
electrons becomes a positively charged ion; the chemical bond between
positively charged and negatively charged ions is called an ionic bond.
2) sharing of electrons with another atom or atoms - the chemical bond
formed is called a covalent bond.

2.1.1 The Ionic Bond.

An ionic bond is formed by the transfer of an electron (or electrons) from one
atom to another. How do we know which atoms gain electrons and which ones lose
electrons? Atoms having low ionization energy (IE) lose electrons easily. Ionization
energy is the amount of energy required to remove the most loosely held electron from
an isolated atom in its ground state.
Atom + Energy (IE) Atom+ + e-
The alkali metals found at the far left of the periodic table have low ionization
energy and so give up electrons easily. Across a period, from left to right of the
periodic table, there is a general increase in ionization energy of the representative
elements.
Atoms that have high electron affinity (EA) gain electrons easily. Electron
affinity is the amount of energy released when an electron is added to an isolated
atom in its ground state.

Atom + e- Atom- + Energy (EA)

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 Republic of the Philippines
CENTRAL BICOL STATE UNIVERSITY OF AGRICULTURE
San Jose, Pili, Camarines Sur 4418
Website: www.cbsua.edu.ph
Email Address: op@cbsua.edu.ph
Trunkline: (054) 871-5531-33 local 101

In general, electron affinity of representative elements increases in going from

left to right of the periodic table. The halogens which appear at the right side of the
periodic table have high electron affinity and so gain electrons easily.

Sodium chloride is formed through ionic bonding between the elements’ sodium
and chlorine.

Sodium has low ionization potential and so readily loses one electron to form
Na which has the electron configuration of the noble gas neon. Chlorine has high
electron affinity and readily gains one electron. It has seven electrons in its valence
shell and needs only one more to make an octet. Chlorine thus readily accepts one
electron from sodium and becomes Cl- which has the electron configuration of the
noble gas argon.
Notice that ionic bonding occurs when electrons transfer from atoms of a metal
to atoms of a nonmetal. The transfer of electrons from atoms of metals to atoms of
nonmetals to form ions is possible because metals have low ionization energy while
nonmetals have high electron affinity.

Before proceeding to the next section, make sure that the formation of an
ionic bond is quite clear to you - what is it, why and how it forms.

2.1.2 The Covalent Bond.

A covalent bond is formed through the sharing of electrons by two atoms. The
formation of the hydrogen molecule is the simplest example of the formation of a
covalent bond. When two hydrogen atoms combine, the electron from one atom
combines with the electron of the other to form an electron pair. The shared electrons
now belong to both hydrogen atoms - a situation similar to a joint bank account.

Each of the two atoms in a covalent bond uses the two electrons in the bond
to acquire a noble gas electron configuration. Thus, each hydrogen atom in the
hydrogen molecule acquires the electron configuration of the noble gas helium.

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 Republic of the Philippines
CENTRAL BICOL STATE UNIVERSITY OF AGRICULTURE
San Jose, Pili, Camarines Sur 4418
Website: www.cbsua.edu.ph
Email Address: op@cbsua.edu.ph
Trunkline: (054) 871-5531-33 local 101

Atoms in the middle of the periodic table will require too much energy to gain
or lose sufficient electrons in order to attain the electron configuration of the noble
gases.
These atoms acquire completely filled outermost shells by sharing electrons,
as shown in the following examples.

In Lewis structures, a covalent bond is indicated by a pair of dots that lie

between the two bonded atoms. As a shorthand notation, a pair of electrons in a
covalent bond is shown as a dash or a short line between the bonded atoms; an
unshared electron pair (lone pair) is shown as a pair of dots. Let us now rewrite the
structures of methane, ammonia and water (shown above) using the line and lone-
pair notation.

An atom can form as many covalent bonds with other atoms as the maximum
number of electrons needed to fill its valence shell

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 Republic of the Philippines
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San Jose, Pili, Camarines Sur 4418
Website: www.cbsua.edu.ph
Email Address: op@cbsua.edu.ph
Trunkline: (054) 871-5531-33 local 101

Hydrogen with one valence electron needs one electron to fill its valence shell
and therefore can form one covalent bond. Carbon with four valence electrons, needs
four more to fill its valence shell and therefore forms four covalent bonds.
By similar reasoning, nitrogen with five valence electrons forms three covalent
bonds; oxygen with six valence electrons forms two covalent bonds; and the halogens
(F, Cl, Br, I) with seven valence electrons form one covalent bond.
Below are some examples which illustrate these different bonding capacities.

methyl amine methyl alcohol methyl bromide

Carbon, nitrogen and oxygen can form more than one bond between a pair of
atoms. Sharing of one electron pair leads to a single bond. Sharing of two electron
pairs leads to a double bond, while sharing of three electrons pairs leads to a triple
bond. The sharing of four electron pairs is not observed.

2.2 WRITING CORRECT LEWIS STRUCTURES FOR POLYATOMIC

IONS AND MOLECULES
Lewis structures are used not only as a simple and convenient notation for
representing the electronic structures of atoms, ions and molecules, but also to
provide an accurate accounting of electrons. Facility with writing correct Lewis
structures is important in the study of organic chemistry.
There are two necessary features for a correct Lewis structure:
1) the electrons in the valence shell of each atom are assigned correctly, and

2) the formal charges are assigned correctly.

Sometimes covalently bonded atoms have a charge; this is called formal

charge. The charge on an atom depends on the number of electrons available to it
and the number of protons in its nucleus.

To determine the number of electrons in the valence shell of an atom, we

count all the electrons of covalent bonds plus any unshared electrons. To assign
formal charge to an atom, we count half of the shared electrons plus any unshared

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 Republic of the Philippines
CENTRAL BICOL STATE UNIVERSITY OF AGRICULTURE
San Jose, Pili, Camarines Sur 4418
Website: www.cbsua.edu.ph
Email Address: op@cbsua.edu.ph
Trunkline: (054) 871-5531-33 local 101

electrons and subtract this number from the number of valence electrons in the
neutral, unbonded atom.
Formal charge = valence electrons of isolated atom - [1/2 shared electrons + unshared
electrons]

Let us assign Lewis structures to the following compounds whose atoms are all
neutral.

1. a compound C3H5N that contains a bond

2. a compound C2H40 that contains a C = O bond

3. a compound C3H4 that contains two C = C bonds

4. a compound C3H4 that contains a C triple bond C

H

H C C C H

5. a compound C2H3Br that contains a C = C bond

We can make certain generalizations about the structures of the uncharged

molecules we have encountered so far:

1) A carbon atom with four covalent bonds is neutral.

2) A nitrogen atom with three covalent bonds and one electron pair is
neutral.
3) An oxygen atom with two covalent bonds and two lone pairs is neutral.

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 Republic of the Philippines
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San Jose, Pili, Camarines Sur 4418
Website: www.cbsua.edu.ph
Email Address: op@cbsua.edu.ph
Trunkline: (054) 871-5531-33 local 101

4) Halogens (F, Cl, Br, I) with one covalent bond and three lone pairs are
neutral.

3.0 CLASSIFICATION OF ORGANIC COMPOUNDS

3.1 CLASSES OF ORGANIC COMPOUNDS

Organic compounds can be classified into two big groups - the hydrocarbons
and those with heteroatoms. The hydrocarbons are organic compounds containing
only hydrogen and carbon.
Elements other than carbon and hydrogen found in organic compounds are
called heteroatoms. Among the most common heteroatoms are oxygen, nitrogen and
the halogens (Cl, Br, I and F). In addition, sulfur and phosphorus are also found in
several organic compounds. Figure 1.1 shows the most common classes of organic
compounds and their relationships with one another.
The hydrocarbons, which contain only carbon and hydrogen, are of two types
the aliphatics and the aromatics. To the aliphatics belong the alkanes, alkenes,
alkynes and their cyclic analogs.

Those with heteroatoms may be grouped according to the heteroatom(s) present, as

follows:
• with halogens - organic halides
• with oxygens - alcohols, phenols, ethers, aldehydes and
ketones, carboxylic acids, anhydrides, esters.
• with nitrogen — amines
• with oxygen and halogen - acid halides
• with oxygen and nitrogen - amides, amino acids.
• with sulfur - thiols, sulfides

One or more hydrogen atoms in the hydrocarbon chain may be replaced by a

heteroatom or a group containing heteroatoms. Since the hydrocarbon portion may
be aliphatic or aromatic, each of the classes above may be of two types for example,
there are aliphatic and aromatic halides, aliphatic and aromatic amines, etc.

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 Republic of the Philippines
CENTRAL BICOL STATE UNIVERSITY OF AGRICULTURE
San Jose, Pili, Camarines Sur 4418
Website: www.cbsua.edu.ph
Email Address: op@cbsua.edu.ph
Trunkline: (054) 871-5531-33 local 101

ORGANIC COMPOUNDS

Figure 1.1 The different classes of organic compounds

3.2 FUNCTIONAL GROUPS

The basis for classifying organic compounds into classes (or families) is
structure. With the exception of the alkanes, each class contains at least one
functional group. The functional group is the atom or group of atoms that defines the
structure and at the same time determines the properties of a class or family of
organic compounds. The behavior of a functional group, whether found in a small, big
or quite complex molecule, is very nearly the same. This means that compounds in
the same class have physical and chemical properties which are quite similar. A large
part of organic chemistry is just the chemistry of functional groups. This is something
for which we can all be thankful, because it enables us to study a few compounds as
representatives of a large number of others. This way, we can learn the

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 Republic of the Philippines
CENTRAL BICOL STATE UNIVERSITY OF AGRICULTURE
San Jose, Pili, Camarines Sur 4418
Website: www.cbsua.edu.ph
Email Address: op@cbsua.edu.ph
Trunkline: (054) 871-5531-33 local 101

characteristics of many thousands of compounds by considering only a few. For

instance, there is no need to know and memorize the reactions of each compound
separately. (Remember that there are more than 10 million!) All we need to do is to
look for the functional group in the compound and recall its typical reactions.
Table 1.1 gives the formula/general structure, functional group and an
example of each of the more common and important classes of organic compounds.
A good way to begin your study of organic chemistry is to familiarize yourself with the
functional groups of the different classes of organic compounds. It will be a
tremendous advantage on your part to be able to identify functional groups and
classify a given organic compound at a glance.

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Republic of the Philippines
CENTRAL BICOL STATE UNIVERSITY OF AGRICULTURE
San Jose, Pili, Camarines Sur 4418
Website: www.cbsua.edu.ph
Email Address: op@cbsua.edu.ph
Trunkline: (054) 871-5531-33 local 101

Page 14 of 15
Republic of the Philippines
CENTRAL BICOL STATE UNIVERSITY OF AGRICULTURE
San Jose, Pili, Camarines Sur 4418
Website: www.cbsua.edu.ph
Email Address: op@cbsua.edu.ph
Trunkline: (054) 871-5531-33 local 101

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