MODULE 1

INTRODUCTION TO ORGANIC CHEMISTRY

Learning Outcomes:
1. Define organic chemistry.
2. Trace historical background of organic chemistry.
3. Classify compounds as organic or inorganic.
4. Differentiate properties of organic compounds from inorganic compounds.
5. Write structural formulas of organic compounds.
6. Identify and name functional group in a structural formula.

Course Outline:
1. Organic Chemistry: Defined
2. Atoms, Elements, and Compounds
3. Ways of Drawing Structures Organic Compounds Based on Formulas
4. Overview of the Functional Groups

Organic chemistry deals with scientific study of structure, composition, properties, preparations,
reactions and synthesis of organic compounds.
Organic compounds contain carbon covalently bound to another carbon (C-C) and to other
atoms such as hydrogen (C-H). The carbon atoms form a carbon skeleton or carbon backbone that
has other bonded atoms such as H, N, O, S, and the halogens (F, Cl, Br, and I).

A. IMPORTANCE OF ORGANIC COMPOUNDS

 Carbons are essential parts of all living organisms. It is the precursor to the production of
carbohydrates, proteins, fats which is important in living systems.
 Basic components of many of the cycles that drive the earth, primarily the carbon cycle
including the exchange of carbon between plants and animals in photosynthesis and cellular
respiration.
 All foods are organic compounds
 Photosynthesis is a reaction that makes carbon a part of our food. Carbon is passed along
through food chains and sugar from photosynthesis is modified and combined with other
materials.
 Dead organisms are food for other organisms, or are buried in the earth and converted to fossil
fuels like peat, coal and petroleum.
 Petroleum is the source of fuel and starting material for plastics, fabrics and industrial
chemicals.

B. ETYMOLOGY OF ORGANIC COMPOUND

Swedish chemist Jöns Jacob Berzelius (1807) introduced it to explain
the study of compounds derived from the living resources available in nature.
** Vital Force Theory – living things had a life force
or a vital force – vis-vitalis — that set them apart from non-
living things. This force supposedly enabled living things
to produce certain chemicals. Otherwise, these
chemicals would not be formed.
However, in 1828 Friedrich Wohler, a former
student of Berzelius, was able to synthesize urea using an
inorganic material which disproved the vital force theory.
C. NOTABLE SCIENTIST IN ORGANIC CHEMISTRY
1. Friedrich August Kekule von Stradonitz (1865).
 discovered the benzene ring structure.
 he discovered this structure after days of studying
benzene and trying to determine how and why it reacts
in the way that it does. One night he had a dream of
snakes twisting together until they formed a circle. He
woke up from this dream and realized that benzene was
circular. From there he was able to figure out the structure
of benzene, which led to further discoveries about how
organic compounds react.

2. Jacobus van 't Hoff and Joseph-Achille Le Bel (1874).

 developed an organic molecule modeling system.
 3D stereochemical representation – a system to indicate what way
these atoms were coming off of the carbon
i. Solid line indicates the atom coming up from the carbon
ii. Dashed line indicates that it is going backwards.
 discovered that carbon is a tetrahedral. In other words, carbon can
have four atoms coming off of it.

D. VERSATILITY AND UNIQUENESS OF ORGANIC COMPOUNDS

 Atoms of carbon can unite with one another by sharing one or more pairs of electron to from
chains, both branched and unbranched, or ring molecules.
 Carbon atoms have four valence electrons so it always forms four covalent bonds.
 Organic molecules exhibit isomerism. Even the same number and kind of atoms are present,
different organic compounds can be formed if the arrangement of these atoms is changed.

** Isomers – compounds that have the same molecular formula but

different structures. Although isomers are composed of the same
collection of atoms, they differ in one or more physical or chemical
properties such as color, solubility, or rate of reaction with some
reagents.

E. ORGANIC VS. INORGANIC CHEMISTRY

Some compounds containing carbon, like carbon monoxide (CO), carbon dioxide. (CO2),
carbonic acid (H2CO3), and polyatomic ions like bicarbonate (HCO3), cyanide (CN), cyanate (CNO)
and carbonate (CO2) are considered inorganic substances because their properties resemble those
of inorganic compounds.
ORGANIC INORGANIC
o high melting points (e.g. NaCl: 801°C)
low melting points (e.g. hexane: -95 C)
low boiling points (e.g. hexane: 69°C) high boiling points (e.g. NaCl: 1,413°C)
low solubility in water; high solubility in greater solubility in water; low solubility in nonpolar
nonpolar solvents like gasoline solvents like gasoline
flammable nonflammable
aqueous solutions do not conduct electricity aqueous solutions conduct electricity
exhibit covalent bonding exhibit ionic bonding
do not conduct current conduct electric current
F. CLASSIFICATION OF ORGANIC COMPOUNDS
NATURAL SYNTHETIC
Synthesized in the laboratory thru chemical
Produced naturally by plants or animals
manipulation
Sugars, enzymes, hormones, lipids, antigens,
fatty acids, neurotransmitters, nucleic acids,
Vitamin C, rubbers , plastics
proteins, peptides, amino acids, vitamins,
lectins, some alkaloids and terpenoids, etc.

Matter – anything that occupies space and has mass.

Atoms – basic chemical unit of matter; smallest unit of an
element. Made up of protons, neutrons and electrons.
Subatomic Particles:
1. Proton – positively charged particles
2. Electron – negatively charged particles
3. Neutron – no net charge
Elements – contains a single type of atom. Each elements
consists of different numbers of protons, electrons and
neutrons. The identity of any element is based on the
atomic number. Example: Carbon, Oxygen, Nitrogen, etc.
Identifying the number protons, electrons, and neutrons of an element.
Atomic number = number of electrons = number of protons
Mass number (A) = atomic number + number of neutrons

Protons = 6
Electrons = 6
Neutrons = varies depending on the isotope of the element
Example: Carbon-12 has 6 neutrons, Carbon-13 has 7 neutrons,
and Carbon-14 has 8 neutrons.

** Isotopes - an atom which has the same atomic number as other atoms of the element, but a different
mass number. However, not all elements have only one stable isotope.
Compounds – made up of two or more elements that are chemically
bonded together.
Examples:
1. Methane – consists of 1 carbon bonded with 4 hydrogens
2. Carbon tetrachloride – consists of 1 carbon bonded with 4
chlorines

A. Type of Chemical Bonds

Chemical Bonding refers to the formation of a chemical bond between two or more atoms,
molecules, or ions to give rise to a chemical compound. These chemical bonds are what keep the
atoms together in the resulting compound.
As mentioned, the positive charged nucleus is
surrounded by electrons arranged in concentric layers
called the energy levels of energy shells. In each level, it
can only accommodate certain number of electrons.
The chemical properties of an element are largely
determined by the number of electrons in their outermost
shells (valence electron). An element is said to be stable
(i.e. it can no longer participate in a chemical reaction)
when its valence electron shell is full.

1. Metallic Bonding
 found in metals and involves the sharing of
a "sea" of electrons between metal atoms.
The electrons are not associated with any
specific atom, but instead move freely
through the lattice of metal atoms, giving
metals their unique properties such as high
conductivity and ductility.

2. Hydrogen Bonding
 occurs between a hydrogen atom
covalently bonded to an electronegative
atom (such as nitrogen, oxygen, or
fluorine) and another electronegative
atom in a nearby molecule. This results in a
weak, but important type of
intermolecular bonding that helps to
stabilize the structures of molecules like
DNA and proteins.

3. Ionic Bonding
 involves the transfer of electrons between metal and non-metal atoms.
 Metal atom loses an electron(s) to form a positively charged ion (cation), while the non-
metal gains electron(s) to form a negatively charged ion (anion).
 The resulting oppositely charged ions attract each other to form a stable ionic compound.

4. Covalent Bonding
 sharing of electrons between two non-metal atoms.
 Atoms that share electrons equally form a nonpolar covalent bond
 Atoms that share unequally form a polar covalent bond
 Rules of covalent bonding:
1. Duet Rule
 hydrogen and helium may have no more than two electrons in their valence shells.
2. Octet Rule
 atoms are most stable when their valence shells are filled with eight electrons.
 Exception to the rule:
i. Those that have an incomplete octet in its valence shell
ii. Those that have an odd number of valence electrons (Free Radicals)
iii. Those that can accommodate more than eight electrons in its valence shells

B. Lewis Dot Structure/Formula

Lewis structure give connectivity of the location of all bonding and non-bonding electrons,
as well as formal charges. However, it does not give information about the 3-dimentional
orientation in space.
General rule:
1. Take the sum of valence e- for all atoms.
2. Arrange atoms in the proper orientation.
3. Hydrogen atoms are terminal atoms.
4. Carbon atoms are generally central atoms.
5. Distribute e- by playing bonds between
atoms (1 bond is equal to 2 e-).
6. Use remaining e- to satisfy the duet rule for H
and the octet rule for the 2nd row elements.
7. If all valence e- are used and an atom does
not have an octet, form multiple bonds
where possible.

C. Intermolecular Forces
Organic compounds are molecules that contain carbon atoms bonded to hydrogen atoms
and other atoms such as oxygen, nitrogen, and halogens. The intermolecular forces in organic
compounds play a critical role in determining their physical and chemical properties, such as
boiling point, melting point, solubility, and reactivity.
The three main types of intermolecular forces that occur in organic compounds are:
1. Van der Waals Forces
 weak, temporary dipole-dipole interactions that arise due
to fluctuations in electron distribution within molecules.
 weakest intermolecular force and are present in all
molecules.
 responsible for the attraction between nonpolar
molecules, such as hydrocarbons, and contribute to their
low boiling points and volatility.

2. Dipole-Dipole Interactions
 stronger than van der Waals forces and occur between polar
molecules, where there is an asymmetrical distribution of charge
within the molecule.
 The partially positive end of one molecule is attracted to the
partially negative end of another molecule, resulting in a dipole-
dipole interaction.
 Examples of polar organic molecules include alcohols and amines.
 2. Hydrogen Bonding
 a specific type of dipole-dipole interaction that
occurs between a hydrogen atom bonded to an
electronegative atom (such as oxygen or nitrogen)
and another electronegative atom in a nearby
molecule.
 Hydrogen bonding is stronger than dipole-dipole interactions and contributes to
the high boiling points and solubility of many organic compounds, such as
alcohols and carboxylic acids.

A. Molecular formula shows the number of each type of atom that is present in the molecule of the
compound.

B. Structural Formula shows the details of the bonding present in the molecule, i.e., which atoms are
connected to which other atom.

1. Full or Expanded Structural Formula – all the atoms and bonds are indicated.
Example: Propane

2. Condensed Structural Formula – an abbreviated form of writing formulas showing no bonds.

Example: Propane – CH3CH2CH3

3. Line Structural Formula – uses lines to show the structure of the compound where each junction
indicates the carbon atom.
Example: Butane
 Carbon combines with other atoms to form characteristic structural units called functional
groups. Functional groups are important for three reasons:
1. They are the units by which we divide the organic compounds into classes.
2. Serve as a basis for naming organic compounds.
3. Characterizes the chemical (sites of chemical reaction) and physical properties of the
molecule.
Type of Compound General Formula Suffix
Alkanes CnH2n+2 -ane
Alkenes CnH2n -ene
Alkynes CnH2n-2 -yne
Aromatic Hydrocarbons C6H6 -benzene
Alkyl Halides RX none
Alcohols ROH -ol

Aldehydes -al

Ketones -one

Ethers -ether

Carboxylic Acids -oic acid

Esters -oate

Amides -amide

Amines -amine

Thiols R-SH none