1

DISCUSSION
STRUCTURE AND BONDING OF
ORGANIC COMPOUNDS
ORGANIC CHEMISTRY
What is organic chemistry? If you just look around us, you will find the answer the food you
eat, the clothing you wear, the medicine you take, are organic chemicals. Likewise, pesticides,
plastics and other polymers, synthetic fibers, dyes, paints, perfumes, flavors, petroleum and a
lot more, are organic chemicals. The stuff of life itself are organic chemicals. There can be no
doubt that most substances which make up our environment belong to the realm of organic
chemistry.

Organic Chemistry is the study of carbon-containing compounds. The term organic was coined
in 1807 by the Swedish chemist Jons Jakob Berzelius. At that time it was thought that all
organic compounds. All early attempts to synthesize these compounds in the laboratory failed,
and it was thought that a vital force, available only in living cells, was needed for their formation.

This idea began to change in 1828 when a twenty-seven-year-old German physician, whose
first love was chemistry, synthesized the organic molecule urea from inorganic starting
materials. This man was Friedrich Wohler, the “father of organic chemistry.”

As a child, Wohler didn’t do particularly well in school because he spent so much time doing
chemistry experiments at home. Eventually, he did earn his medical degree, but he decided to
study chemistry in the laboratory of Berzelius rather than practice medicine.

After a year he returned to Germany to teach and, as it turned out, to do the experiment that
made him famous. The goal of the experiment was to prepare ammonium cyanate from a
mixture of potassium cyanate and ammonium sulfate. He heated a solution of two salts and
crystallized the product. But the product didn’t look like ammonium cyanate. It was a white
crystallized material that looked exactly like urea! Urea is waste product of protein breakdown in
the body and is excreted in the urine. Wohler recognized urea crystals because he had
previously purified them from the urine of dogs and humans. Excited about his accidental
discovery, he wrote to his teacher and friend Berzelius, “I can make urea without the necessity
of a kidney, or even an animal, whether man or dog.”
O
+ - heat ||
NH4 O C N H2O – C – NH2
ammonium cyanate urea

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This finding dealt a severe blow to the theory of vital force and was particularly significant in the
history of organic chemistry for its demonstrated that inorganic substances could be converted
to organic substances. In 1845, Kolbe synthesized acetic acid from the elements, and in 1856,
Berthelot synthesized methane. With the weight of these evidences, the theory of vital force was
finally died in the mid-19th century.
At present, over 10 million organic compounds have been characterized and this number is
increasing by a half million each year in two ways: 1) by the isolation of anew natural product,
and 2) by the chemical synthesis of a new compound.

Chemistry today is unified – the basic scientific principles that explain the simplest inorganic
compounds also explain the most complex organic molecules. However, the division between
organic and inorganic chemistry, which began for historical reasons is maintained for
convenience.

How do we define organic chemistry today? Simply it is the study of the compounds of
carbon.

The Nature of Organic Compounds

Kekule (Germany) and Couper (Scotland) were the first to recognize that carbon is tetravalent –
it can form four covalent bonds, not only with other elements (mainly H, O, N) but also with other
carbon atoms. The most distinctive feature of carbon atoms is their capacity to form very strong
covalents bonds with each other. No other element, including silicon, can do this. Silicon-silicon
bonds are easily cleaved. Silicon-oxygen-silicon bonds are quite strong but do not result in the
incredible diversity found in carbon compounds.

Why are there so many organic compounds? There are several reasons. Carbon compounds
can link with each other to form linear, branched or cyclic backbones for a wide variety of
organic molecules. For example:
C
| C C
C–C–C–C–C C–C–C
| C C
C
C
linear 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 C
single bond double bond triple bond

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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 different structural formulas, i.e., the same atoms
can be put together in different ways so as to result in different compounds with entirely different
properties. For example, two structural formulas can be derived from the molecular formula
C2H6O, and each one corresponds to a real compound.
H H H H
| | | |
H C C O H H C O C H
| | | |
H H H H
ethyl alcohol dimethyl ether
liquid: bp 78.5 ºC gas: bp – 23.7 ºC

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 stuctures.

Let us take the case of the amino acid alanine, whose structural formula is a given below:
H
|
CH3 C C 0 0H
|
NH2
alanine

Alanine can have two different three-dimensional structures which are mirror images of each
other.
CH3 CH3

C C
H H
NH2 C 0 0H H00C NH2

L – alanine D – alanine

The amino acids that make up the proteins of our bodies all have to be the L – series; our
bodies will not be able to utilize D-amino acids.

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At this point you have probably realized that carbon is indeed very versatile and why it is so. It
should now be east 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 immediately decomposes extensively and is turned to carbon.

Electronics 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 symbols is surrounded
by a number of dots equal to the number of valence electrons.

EXAMPLE 1
QUESTION. Write the Lewis structure of the first 18 elements

ANSWER

IA II A III A IV A VA VI A VII A VIII A

PERIOD

1 H· He :

. . . . . ..
2 Li · B: B: .C: .N: :O: :F: : Ne :
` ` `` ``

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. . . . . ..
3 Na · Mg : Al : . Si : :P: :S: : Cl : : Ar :
` ` ` `` ``

Notice that the noble gases – helium, neon and argon – have completely filled valence shells.
The valence shell of helium has two electrons, while those of neon and argon have eight
electrons (octet). The valence shell of the other elements in the above table are only partially
filled. Notice also that the number of valence electrons of an atom corresponds to its group
number in the periodic table; helium is an exception.

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 electronic configuration of these elements (the noble gases have
completely filled valence shells). Lewis than 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 as 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 shells:

1) Gaining or losing enough electrons; an atom that gains electrons become a

negatively charged ion, on the other hand an atom that loses electrons becomes a
positively 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.

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 gains electrons and which one lose electrons? Atoms having low
ionization potential (IP) lose electrons easily. Ionization potential is the amount of energy
required to remove the most loosely held electron from an isolated atom in its ground state.

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Atom + Energy (IP) Atom+ + (electron)-

The alkali metals found at the far left of the periodic table have low ionization potential and so
give up electrons easily. Across a period, from left to right of the periodic table, there is a
general increase in ionization potential of the representative elements.
On the other hand, atoms having 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 + (electron)- Atom- + Energy (EA)

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

The formation of sodium chloride from the elements sodium and chloride is an example of ionic
bond formation.
.. .. _
Na· + . Cl : Na+ : Cl :
*

Sodium has a low ionization potential and so readily loses one electron to form Na+ which then
acquires the electronic configuration of the noble gas neon.

Chlorine has a high electron affinity (EA) and readily gains just one electron because it has
seven electron because it has seven electrons in its valence shell and needs only one more to
make a complete octet. Therefore, chlorine readily accepts one electron from sodium and
becomes C1- and thus acquires the electronic configuration of the noble gas argon.

? SAQ 1
1. For each of the following reactions, the elements combine through transfer of one or
more electrons, resulting in a completely filled outermost shell form each atom. Draw
Lewis structures for each atom, assigning the correct number of valence electrons and
the correct charges.

a. Li + F Li F
b. K + Br KBr
c. Mg + O Mg O
d. 2Li + O Li O Li
e. Ca + 2Cl Cl Ca Cl

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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.

H·+·H H:H

Each of the two atoms in a covalent bond uses the two electrons in the bond to acquire a noble
gas electronic configuration. Thus, each hydrogen atom in the hydrogen molecule acquires the
configuration of the noble gas helium.
Atoms in the middle of the periodic table will require too much energy to gain or lose sufficient
electrons in order to attain the electronic configuration of the noble gases.
These atoms acquire completely filled outermost shells by sharing electrons, as shown in the
following examples.
. H
4 H·+·C· H:C:H
*
H
methane
.. ..
3 H · + · Na · H:N:H
*
H
Ammonia

.. ..
2 H·+·O· H:O:H
** **
water

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
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.

H
| •• ••
H–C–H H–N–H H–O–H
| |
H H

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methane ammonia water

The Covalence of the More Common Atoms Found In Organic Molecules

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

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.

H H H
| .. | .. |
H–C–N–H H–C–O–H H – C – Br
| | | ** |
H H H H
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.

EXAMPLE 1
QUESTION Write all the Lewis structures in which two carbon atoms are bonded to each other
and the remaining carbon bonds are formed to hydrogen atoms.

ANSWER: If the carbon – carbon linkage is a single bond, each carbon atoms must form three
bonds to hydrogen. The result is ethane, C2H6.
H H
• • | |
• C – C • + 6 H• H–C–C–H
• • | |
H H
ethane

If the carbon-carbon linkage is a double bond, each carbon atom must form two bonds to
hydrogen. The result is ethylene, C2H4.
H H
: C = C : + 4H · C=C

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H H
If the carbon-carbon linkage is a triple bond, each carbon atom must form one bond to
hydrogen, The result is acetylene, C2H2.

•C C • + 2 H• H–C C–H
acetylene

Empirical and Molecular Formula Determination

The empirical formula, which expresses the relative numbers of the different atoms present in
a molecule, can easily be calculated from the data on elemental analysis.

The molecular formula, which expresses the actual number of each kind of atom present, can
be derived from the empirical formula. The molecular formula may be the same as the empirical
formula or some multiple of it. In order to derive the molecular formula from the empirical
formula, the molecular weight (molecular mass) of the compound being analyzed should be
determined.

There are several ways of determining molecular weight. For gaseous organic compounds and
liquid substances of moderate volatility, molecular weights may be determined by vapor-density
experiments. Molecular weights of high-boiling liquids and slightly volatile solids are determined
by measurements of freezing-point depressions or boiling-point elevations. Highly accurate
molecular weights may be determined by mass spectrometry.

Calculating Empirical Formulas

The following steps in calculating empirical formula:
Step 1. Assume a definite starting quantity (usually 100.0 g) of the compound, if not given and
express the mass of each element in grams.

Step 2. Convert the grams of each element into moles using each element’s molar mass. This
conversion gives the number of moles of atoms of each element in the quantity assumed in
Step 1. At this point, these numbers will usually not be whole numbers.

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Step 3. Divide each value obtained in Step 2 by the smallest of these values. If the numbers
obtained are whole numbers, use them as subscripts and write the empirical formula. If the
numbers obtained are not whole numbers, go on Step 4.
Step 4. Multiply the values obtained in Step 3 by the smallest number that will convert them to
whole numbers. Use these whole numbers as the subscripts in the empirical formula. For
example, if the ratio of A to B is 1.0 : 1.5, multiply both numers by 2 to obtain a ratio of 2:3. The
empirical formula then is A2B3.

EXAMPLE 1
Calculate the empirical formula of a compound containing 11.19 % hydrogen (H) and 88.79 %
oxygen (O):

Step 1. Express each element in grams. Assuming 100.0 g of material, we know that the
percent of each element equals the grams of each element and that the percent sign can be
omitted:
H = 11.19 g
O = 88.79 g

Step 2. Convert the grams of each element to moles:

H: (11.19 g H) (1 mol H atoms) = 11.10 mol H atoms

1.008 g H
O: (88.79 g O) (1 mol O atoms) = 5.549 mol O atoms
16.00 g O

The formula could be expressed as H11.10O5.549. However, it’s customary to use the
smallest whole-number ratio of atoms. This ratio is calculated in Step 3.

Step 3. Change these numbers to whole numbers by dividing them by the smaller number:

H = 11.10 mol = 2.000 O = 5.549 mol = 1.000

5.549 mol 5.549 mol

In this step, the ratio of atoms has not changed, because we divided the number of
moles of each element by the same number:

The simplest ratio of H to O is 2 : 1.

Empirical formula = H2O

EXAMPLE 2
The analysis of a salt shows that it contains 56.58 % potassium (K); 8.68 % carbon (C); and
34.73 % oxygen (O). Calculate the empirical formula for this substance.

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Step 1 and 2. After changing the percentage of each element to grams, we find the relative
number of moles of each element by multiplying by the proper conversion factor:
K : (56.58 g K) (1 mol K atoms) = 1.447 mol K atoms
39.10 g K

C : (8.68 g C) (1 mol C atoms) = 0.723 mol C atoms

12.01 g C

O : (34.73 g O) (1 mol O atoms) = 2.171 mol O atoms

16.00 g O

Step 3. Divide each number of moles by the smallest value:

K = 1.447 mol = 2.00

0.723 mol

C = 0.723 mol = 1.00

0.723 mol

O = 2.171 mol = 3.00

0.723 mol

The simplest ratio of K : C : O is 2 : 1 : 3.

Empirical formula = K2CO3

EXAMPLE 3
A sulfide of iron was formed by combining 2.233 g of iron (Fe) with 1.926 g of sulfur (S). What is
the empirical formula of the compound?

Step 1 and 2. The grams of each element are given, so we use them directly in our calculations.
Calculate the relative number of moles of each element by multiplying the grams of each
element by the proper conversion factor:

Fe : (2.233 g Fe) (1 mol Fe atoms) = 0.03998 mol Fe atoms

55.85 g Fe

S : (1.926 g S) (1 mol S atoms) = 0.06006 mol S atoms

32.07 g S

Step 3. Divide each number of moles by the smaller of the two numbers:

Fe = 0.03998 mol = 1.0000 S = 0.06006 mol = 1.502

0.03998 mol 0.03998 mol

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Step 4. We still have not reached a ratio that gives whole numbers in the formula, so we double
each value to obtain a ratio of 2.000 Fe atoms to 3.000 S atoms. Doubling both values does no
change the ratio of Fe and S atoms:

Fe : (1.000) 2 = 2.000
S : (1.502) 2 = 3.004
Empirical formula = Fe2S3

?
SAQ 2
1. Calculate the empirical formula of a compound containing 52.14 % C, 13.12 % H, and
34.73 % O.

2. Calculate the empirical formula of a compound that contains 43.7 % phosphorus and
56.3 % O by mass.

Calculating the Molecular Formula from the Empirical Formula

The molecular formula can be calculated from the empirical formula if the molar mass is known.
The molecular formula, will be equal either to the empirical formula or some multiple of it. For
example, if the empirical formula of a compound of hydrogen and fluorine is HF, the molecular
formula can be exmpressed as (HF)n, where n = 1, 2, 3, 4, …. This n means that the molecular
formula could be HF, H2F2, H3F3, H4F4, and so on. To determine the molecular formula, we must
evaluate n:

n= molar mass = number of empirical formula units

mass of empirical formula

What we actually calculate is the number of units of the empirical formula contained in the
molecular formula.

EXAMPLE 1
A compound of nitrogen and oxygen with a molar mass of 92.00 g was found to have an
empirical formula of NO2. What is its molecular formula?

SOLUTION. Let n be the number of NO2 units in a molecule; then the molecular formula is
(NO2)n. each NO2 unit has a mass of [14.01 g + 2(16.00 g)] or 46.01 g. The molar mass of
(NO2)n is 92.00 g, and the number of 46.01 units in 92.00 is 2;

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n = 92.00 g = 2 (empirical formula units)

46.01 g

N2O4 The molecular formula is (NO2)2 or N2O4.

EXAMPLE 2
Propylene is a compound frequently polymerized to make polypropylene which is used for rope,
laundry bags, blankets, carpets and textile fibers. Propylene has a molar mass of 42.08 g and
contains 14.3 % H and 85.7 % C. What is its molecular formula?

SOLUTION. First find the empirical formula:

C : (85.7 g C) (1 mol C atoms) = 7.14 mol C atoms

12.01 g C

H : (14.3 g H) (1 mol H atoms) = 14.2 mol H atoms

1.08 g H

C3H6 Divide each value by the smaller number of moles:

C = 7.14 mol = 1.00

7.14 mol

H = 14.2 mol = 1.99

7.14 mol

Empirical formula = CH2

We determine the molecular formula from the empirical formula and the molar mass:

Molecular formula = (CH2)n

Molar mass = 42.08 g

Each CH2 unit has a mass of (12.01 g + 2.016 g) or 14.03 g. The number of CH 2 units in 42.08 g
is 3:

n = 42.08 g = 3 (empirical formula units)

14.03 g

The molecular formula is (CH2)3, or C3H6.

?
SAQ 3
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1. Calculate the empirical and molecular formulas of a compound that contains 80.0 % C,
20.0 % H, and has a molar mass of 30.00 g.

Summary
There are millions of organic compounds – much more than the combined compounds of the
rest of the elements in the periodic table. This number is increasing tremendously as more new
compounds are isolated from natural sources and synthesized in the laboratory.

Carbon is tetravalent, i.e., it can form four covalent bonds with other carbon atoms as well as
other elements mainly H, O, N.

Carbon atoms can link with each other to form linear, branched or cyclic chains. In addition,
carbon atoms may participate in single, double or triple bonds. These properties of carbon
atoms plus the fact that organic compounds exhibit isomerism, explain the huge number of
organic compounds and the great diversity in their structure.

Atoms bond together in such a way that each atom participating in the bond acquires the very
stable electronic configuration of the noble gases. Carbon atoms acquire an octet of electrons
by sharing electrons with other atoms. Thus, organic compounds are mostly covalent
compounds having low melting points and limited solubility in water.

Empirical and molecular formulas of organic compounds can be calculated from experimental
data. There are several structural formulas that correspond to a single molecular formula. To
know which is the actual structure of the compound being analyzed will require careful analysis
of its physical and chemical properties.

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References
Brown, W. H. 1982. Introduction to Organic Chemistry, (3 rd edn.) Boston: Willer
Grant Press

Carry, F. A. 1992. Organic Chemistry, (2nd edn. New York: McGraw-Hill, Inc.

McMurry, J. 1988. Organic Chemistry, (2 nd edn.) California: Brooks/Cole Publishing

Co.

Morrison, R.T. and R. N. Boyd. 1987. Organic Chemistry, (5 th den.) Boston: Allyn and
Bacon

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ANSWERS TO SELF-ASSESMENT QUESTIONS

(ASAQ)
SAQ 1
1) REMEMBER: The number of valence electrons of a neutral free atom corresponds to its
group number in the periodic table.
•• ••
+
a. Li • + • F : Li : F :
•• ••
•• •• -
b. K • + • Br : K+ : Br :
•• ••
• •• •• -2
2+
c. Mg • + • O : Mg : O :
• ••
•• •• -2
d. 2 Li • + • O : Li : O : Li+
+

• ••
• •• •• - •• -
e. Ca • + 2 • Cl : : Cl : Ca2+ : Cl :
•• •• ••

SAQ 2
1) C2H6O
2) P2O5

SAQ 3
1) The empirical formula is CH3; the molecular formula is C2H6.

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Structure and Bonding of Organic Compounds

MASTERY TEST

1. For each of the following reactions, the elements combine through transfer of one or
more electrons, resulting in a completely filled outermost shell form each atom. Draw
Lewis structures for each atom, assigning the correct number of valence electrons and
the correct charges.
a. Na + Cl NaCl
b. Zn + O ZnO
c. Mg + 2I IMgI
Solve the following problems:

2. Ascorbic acid (Vitamin C) contains 40.92 % C, 4.58 % H, and 54.50 % O by mass. What
is the empirical formula of ascorbic acid?

3. Mesitylene, a hydrocarbon that occurs in small amounts in crude oil, has an empirical
formula of C3H4. The experimentally determined molecular weight of this substance is
121. What is the Molecular formula of Mesitylene?

4. Ethylene glycol, the substance used in automobile antifreeze, is composed of 38.7 % C,

9.7 % H, and 51.6 % O by mass. Its molar mass is 62.1 g/mol.
a) What is the empirical formula of ethylene glycol?
b) What is its molecular formula?

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