Module in Organic Chemistry: Aklan State University

Republic of the Philippines
Aklan State University

Banga, Aklan
Module in
Organic Chemistry
Volume 1
Hine M a r a e Pa l m a -A r b oleda
Republic of the Philippines
Banga, Aklan
Module in
Organic Chemistry
VOLUME 1
Personal Property of _____________________________________________

Course/Year/Section _____________________________________________
School/College ____________________________________________
In-case this book is lost & found, please contact this no. _________________
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Preface
Welcome to Organic Chemistry! You are about to become
acquainted with one of the most exciting scientific disciplines. This module –
volume 1 provides an introduction to organic chemistry for students who
intend to pursue careers in the sciences and who require a rounding
knowledge in organic chemistry
The volume 1 of this module is divided into three chapters,

Introduction to Organic Chemistry, Organic Molecules and It’s Functional
Group and Alkane. Each chapter contains illustrations and trables including
comprehensive explanation, completed with examples and problem sets.
All of the examples are presented in a style that is easy to understand.
While studying with this module, you will realize that organic
chemistry is a tool for many discipline, and that organic compounds, both
natural and synthetic, are all around you in pharmaceuticals, plastics, fibers,
agrochemicals, surface coatings, toiletry preparations and cosmetics, food
additives, adhesives, and elastomers. Furthermore, you will recognize that
organic chemistry is a dynamic and ever-expanding area of science waiting
openly for those who are prepared, both by training and an inquisitive
nature, to ask questions and explore.
The compiler of this module is excited to bring you an ever-expanding

understanding of this magnificent subject! Learning organic chemistry is not
easy peasy but it can be fun if you put your mind and heart to it. You will
discover that organic chemistry is a synthetic science, which merge the
principles of general chemistry, and biology. Thus, a more advanced and
creative kind of thinking is needed to gain a deeper understanding of this
course.
Contents
Introduction
Chapter Objectives 1
Writing and Naming Chemical Formula 2
Reference 6
Problem Set 7
Chapter 1 Introduction to Organic Chemistry

Lesson 1 What is Organic Chemistry? 9

Lesson 2 The Carbon Atom and its C–C Bond 11
Reference 17
Problem Set 19
Chapter 2 Organic Molecules and It’s Functional Group

Lesson 1 The Functional Group 21
Lesson 2 Physical Properties 23

Reference 24
Problem Set 25
Chapter 3 Alkane
Lesson 1 IUPAC System of Nomenclature 27

Lesson 2 Naming of Alkane 28
Lesson 3 Alkanes Around Us 31

Lesson 4 Physical and Chemical Properties of Alkanes 34
Reference 35
Problem Set 37
Introduction
Objectives
1. Write chemical formula
2. Name binary and tertiary compounds
Writing and Naming Chemical Formula

Chemical nomenclature ensures that a spoken or written chemical name leaves no vagueness or
misinterpretation to what chemical compound name refers to. Every chemical name refers to a specific
substance. But most scientist of today use common name rather than its IUPAC name such as water
instead dihydrogen oxide (H2O) or lime instead of calcium hydroxide [Ca(OH) 2].
IUPAC or International Union of Pure and Applied Chemistry established the widely known and
accepted format of nomenclature for chemical formulas. It name substances in a systematic method.
1.1 WRITING CHEMICAL FORMULAS

A chemical formula represents the relative numbers of elemental atoms in a chemical
compound. It consists of elemental symbol and subscript number which depict the number of
atoms a certain compound compose of. The formula itself will determine the type of substance,
its composition, and its properties.
Formulas of Binary Ionic Compounds

An ionic compound formula must satisfy the octet rule. Octet rule states that atoms below
atomic number 20 tend to combine so that they each have eight electrons in their valence shell, which
gives them the same electronic configuration as a noble gas. The rule is applicable to the main- group
elements, especially carbon, nitrogen, oxygen, and the halogens, but also to metals such as sodium and
magnesium.
Ionic bonds are formed when metal transfers of one or more valence electrons to non-metal.
The transfer of electrons will achieve a stable electronic configuration by having eight electrons in the
outermost valence shell following the octet rule.
The complete formula for an ionic compound can be determined by satisfying two conditions:
1 The charge of an ion can be determined based on the transfer of valence electrons necessary in
order to satisfy the octet rule.
2 An electrically neutral compound is formed when cations and anions combined.
1
No part of this module may be reproduced, stored in a retrieval system or transmitted in any form or by any means, mechanical, electronic,
photocopying, recording or otherwise without the prior written permission of the author/s.
This module is distributed for the students of Aklan State University intended for academic purposes only
For example: Magnesium and Sulfur
Potassium and Sulfur
Formulas of Ternary Ionic Compounds

Metals and polyatomic ions are required in the formation of ternary ionic compounds.
Polyatomic ions are group of covalently bonded atoms with an overall charge, making them an ion. It
behaves as a single unit, thus can form ionic bond with metals.
For example: Potassium and sulfate ion
Common Polyatomic Ions
Cations Anions
Ammonium NH4+ Cyanide CN-
Hydronium H3O+ Cyanate OCN-
Mercury (I) Hg22+ Carbonate CO32-
Anions Chromate CrO42-
Hypochlorite ClO- Dichromate Cr2O72-
Chlorite ClO2- Sulfite SO32-
Chlorate ClO3- Sulfate SO42-
Perchlorate ClO4- Oxalate C2O42-
Acetate C2H3O2- Biphosphite HPO32-
Nitrite NO2- Biphosphate HPO42-
Nitrate NO3- Thiosulfate S2O32-
Bicarbonate HCO3- Peroxide O22-
Permanganate MnO4- Phosphite PO33-
Bisulfite HSO3- Phosphate PO43-
Bisulfate HSO4- Arsenate AsO43-
2
Hydroxide OH- Silicate SiO44-
1.2 NAMING CHEMICAL FORMULAS
Ionic Compounds
Ionic compound is a chemical compound containing cation and anion that are held together by
ionic bonds. The positively charged portion is a metal cation and the negatively charged portion is an
non-metal anion or polyatomic ion.
The Stock Method of Naming

An ionic compound is named first by its cation and then followed by its anion.
 The cation has the same name as its element.
o Na+1 is called the sodium ion, just as Na is called the sodium atom
 The anion is named by taking the elemental name, removing the ending, and adding “-ide.”
o Cl-1 is called chloride, for the elemental name, chlorine, “-ine” was removed and replaced
with “-ide.”
To name the ionic compound, the cation name and the anion named are added together. For example,
NaCl is also known as sodium chloride.
If the cation or the anion is a polyatomic ion, then, the polyatomic ion name is used. For example,
Ba(NO3)2 is called barium nitrate.
For cations with multiple charges or oxidation number (typically transition metals), the charge is written
using Roman numeral in a parenthesis after the elemental name.
 For example: Fe(NO3)3 is iron (III) nitrate
o the charge/oxidation number of three nitrate ions (NO3−1) is 3(-1) = -3. Since the net
charge of the ionic compound must be zero, the Fe ion has a 3+ charge.
o The Roman numeral shows the oxidation number, but in simple ionic compounds this
will always be the same as the metal’s ionic charge.
The Old, Classic, or Common Way of Naming

Formula Systematic Name Common Name
CuCl Copper (I) chloride Cuprous chloride
CuCl2 Copper (II) chloride Cupric chloride
Hg2Cl2 Mercury (I) chloride Mercurous chloride
HgO Mercury (II) oxide Mercuric chloride
FeS Iron (II) sulfide Ferrous sulfide
Fe2S3 Iron (III) sulfide Ferric sulfide
In older method, the suffixes -ous and -ic to denote the lower and higher charges or oxidation 3
number are used where latin names of the elements are used, for example, ferrous/ferric,
cuprous/cupric. This system is still used, although it has been officially supplanted by the more precise
Stock system. In both systems, the name of the anion ends in -ide.
Covalent or Molecular Compounds
Naming molecular compound uses a systematic approach of prefixes that indicate the number of
each element present in a compound. In IUPAC nomenclature of simple molecular compounds, the more
electropositive atom is written first and the more electronegative element is written last.
 Common exceptions exist for naming molecular compounds, where trivial or common names are
used instead of systematic names, such as ammonia (NH3) instead of nitrogen trihydride or
water (H2O) instead of dihydrogen monooxide.
Rules for Naming Molecular Compounds:

1. Remove the ending of the second element, and add “ide” just like in ionic compounds.
 For example: oxygen = oxide sulfur = sulfide
2. The Greek prefixes are used to dictate the number of a given element present in a molecular
compound.
 For example: ” mono-” indicates one, “di-” indicates two, “tri-” is three, “tetra-” is four,
“penta-” is five, and “hexa-” is six, “hepta-” is seven, “octo-” is eight, “nona-” is nine, and
“deca” is ten.
3. If there is only one of the first element, you can drop the prefix.
 For example, CO is carbon monoxide, not monocarbon monoxide.
4. If there are two vowels in a row that sound the same once the prefix is added (they “conflict”), the
extra vowel on the end of the prefix is removed.
 For example, one oxygen would be monooxide, but instead it’s monoxide. The extra o is
dropped.
Examples of Molecular Compound Names:

 SO2 is called sulfur dioxide
 SiI4 is called silicon tetraiodide
 SF6 is called sulfur hexafluoride
 CS2 is called carbon disulfide
1.3 NAMING ACIDS, BASES, AND HYDRATES
Acid Compounds
Acids are named by the anion they form when dissolved in water. Depending on what anion the
hydrogen is attached to, acids will have different names.
 Simple acids, known as binary acids, have only one anion and one hydrogen.
o These anions usually have the ending “-ide.”
o As acids, these compounds are named starting with the prefix “hydro-,” then adding the 4
first syllable of the anion, then the suffix “-ic.”
o For example, HCl, which is hydrogen and chlorine, is called hydrochloric acid.
 More complex acids have oxygen in the compound.
o Any polyatomic ion with the suffix “-ate” uses the suffix “-ic” as an acid. So,
o When you have a polyatomic ion with one more oxygen than the “-ate” ion, then your
acid will have the prefix “per-” and the suffix “-ic.”
o With one fewer oxygen than the “-ate” ion, the acid will have the suffix “-ous.”
o With two fewer oxygen than the “-ate” ion, the prefix will be “hypo-” and the suffix will
be “-ous.”
 For example:
HClO hypochlorous acid
HClO2 chlorous acid
HClO3 chloric acid
HClO4 perchloric acid
Base Compounds
Most strong bases contain hydroxide, a polyatomic ion. Therefore, strong bases are named
following the rules for naming ionic compounds.
 For example, NaOH is sodium hydroxide, KOH is potassium hydroxide, and Ca(OH) 2 is calcium
hydroxide.
Weak bases made of ionic compounds are also named using the ionic naming system.
 For example, NH4OH is ammonium hydroxide.
Weak bases are also sometimes molecular compounds or organic compounds because they have
covalent bonds. They are named following the rules for molecular or organic compounds.
 For example, methyl amine (CH3NH2) is a weak base.
Hydrates Compounds
“Hydrate” is a term used in inorganic chemistry and organic chemistry to indicate that a substance
contains loosely bonded water. The name of a hydrate follows a set pattern: the name of the ionic
compound followed by a numerical prefix and the suffix “-hydrate.”
 For example, CuSO4 · 5 H2O is “copper(II) sulfate pentahydrate.”
The notation of hydrous compound · nH2O, where n is the number of water molecules per formula unit
of the salt, is commonly used to show that a salt is hydrated.
 The “*latex+\cdot*/latex+” indicates that the water is loosely bonded to the ionic compound.
 The “n” is usually a low integer though it is possible for fractional values to exist.
 The prefixes are the same Greek prefixes used in naming molecular compounds.
 A monohydrate “n” is one; in a hexahydrate “n” is 6, and so on.
The Greek prefixes used in naming hydrates for numbers 1/2 through 10 are as follows:
1/2: hemi- 1: mono- 2: di- 3: tri- 5
4: tetra- 5: penta- 6: hexa- 7: hepta-
8: octa- 9: nona- 10: deca-
References
Books:
th
Brown, et.al.(2015).Chemistry: The Central Science 13 Ed
th
Chang, R. & Overby, J. (2019) Chemistry 13 Ed USA: Mc Graw Hill
Internet:
https://www.toppr.com/guides/physics/atomic-and-molecular-structure/polyatomic-ion-definition-and-examples/
https://courses.lumenlearning.com/boundless-chemistry/chapter/naming-compounds/#:~:text=In%20nomenclature%
20of%20simple%20molecular,present%20in%20a%20molecular%20compound
https://chem.libretexts.org/Bookshelves/Physical_and_Theoretical_Chemistry_Textbook_Maps/Supplemental_Modules_(P
hysical_and_Theoretical_Chemistry)/Electronic_Structure_of_Atoms_and_Molecules/Electronic_Configurations/The
_Octet_Rule
https://courses.lumenlearning.com/boundless-chemistry/chapter/chemical-formulas/
https://chem.libretexts.org/Bookshelves/Physical_and_Theoretical_Chemistry_Textbook_Maps/Supplemental_Modules_(P
hysical_and_Theoretical_Chemistry)/Electronic_Structure_of_Atoms_and_Molecules/Electronic_Configurations/The
_Octet_Rule
https://courses.lumenlearning.com/introchem/chapter/naming-hydrates/
PROBLEM SET
Name____________________________ Course/Year/Section____________ Date______________
1. Write chemical formulas for the compounds in each box

zinc copper (I) iron (III) gallium silver lead (IV)
bromide ZnBr2
acetate
phosphate
oxide
nitride
sulfate
2. Write the formulas for the following compounds:

____________________________________a) copper (II) chloride
____________________________________ b) lithium acetate
____________________________________ c) vanadium (III) selenide
____________________________________ d) manganese (IV) phosphide
____________________________________ e) beryllium sulfide
____________________________________ f) potassium sulfate
____________________________________ g) aluminum arsenide
____________________________________ h) potassium permanganate
____________________________________ i) chromium (VI) cyanide
____________________________________ j) tin (II) sulfite
3. Give the correct IUPAC name of the following chemical formula

____________________________________ a) MoF4
____________________________________ b) NH4NO3
____________________________________c) Au2O
____________________________________d) YBr5 7
____________________________________e) AlF3
4. Write the chemical formula for the following covalent compounds:
______________a) carbon tetrachloride ______________e) sulfur trioxide
______________b) carbon trioxide ______________f) dinitrogen pentoxide
______________c) sulfur hexafluoride ______________g) nitrogen dioxide
______________d) dinitrogen heptaoxide ______________h) phosphorous trichloride
5. Give the correct IUPAC name of the following chemical formula
_____________________________a) BCl3 _____________________________e) SF6
_____________________________b) N2O4 _____________________________f) B2Br4
_____________________________c) PCl5 _____________________________g) SO2
_____________________________d) N2O
6. Write the formula for each of the acid and base listed below:
______________a. Hydrocyanic acid ______________f. Potassium hydroxide
______________b. Acetic acid ______________g. Ammonium hydroxide
______________c. Hydrobromic acid
______________d. Nitrous acid
______________e. Formic acid
7. Give the correct IUPAC name of the following acids and bases listed below:
________________________a) HBO3 ___________________________f. LiOH
________________________b) HI ___________________________g. Ca(CN)2
________________________c) H2S ___________________________h. Sr(OH)2
________________________d) H2CrO4
________________________e) H2CO3
8. Name the following hydrates:
a) CaCl2 ● 8 H2O _________________________________________________
b) FeSO4 ● 6 H2O ________________________________________________
c) LiOH ● H2O __________________________________________________
d) PbCl2 ● 3 H2O _________________________________________________
e) Li2CrO4 ● 5 H2O _______________________________________________
f) Na2SO4 ● 10 H2O ______________________________________________
9. Write the formulas for the following hydrates:
________________________a) Barium Phosphate dehydrate
________________________b) Copper(II)sulfate pentahydrate
________________________c) Cobalt chloride hexahydrate
________________________d) Magnesium sulfate heptahydrate
________________________e) Nickel (II) sulfate hexahydrate
________________________f) Copper (I) Bromide tetrahydrate 8
Chapter 1 Introduction to Organic Chemsitry
Objectives
3. Define and explain Organic Chemsitry
4. Review some ideas about atoms, bonds, and molecular geometry
5. Draw Lewis structures, predict the shape of molecules, determine what orbitals are
used to form bonds, and how electronegativity affects bond polarity
6. Draw organic molecules, both shorthand methods routinely used for simple and
complex compounds, as well as three-dimensional representations
LESSON 1 What is Organic Chemistry?

Organic chemistry is the study of carbon-containing compounds. The term organic was coined in
1807 by the Swedish chemist Jöns Jakob Berzelius. At that time it was thought that all organic
compounds, such as fats, sugars, coal, and petroleum, were formed by living or once living organisms
Perhaps the most remarkable feature of organic compounds is that they involve the chemistry of
carbon and only a few other elements—chiefly, hydrogen, oxygen, and nitrogen. While the majority of
organic compounds contain carbon and just these three elements, many also contain sulfur, a halogen
(fluorine, chlorine, bromine, or iodine), and phosphorus.
1.1 WHAT’S SO SPECIAL ABOUT CARBON?
Historical Significance
 Early beliefs of scientist
O Organic compounds can only be found in living or once living organism such as fats, sugars,
coal, and petroleum and that inorganic compounds were those found in rocks and other non-
living matter
 attempts to synthesize these substances in the laboratory failed
 “vital force” possessed only by living organism to form organic compound
 1828 – Friedrich Wöhler conduct an experiment
O synthesized the organic molecule urea in the laboratory
O organic compounds could be obtained from inorganic materials
O known as “father of organic chemistry”
O few years later, August Kekulé (1829–1896) put forth a new definition—organic compounds
are those containing carbon—and his definition has been accepted ever since
Number of Organic Compounds

 more than 10 million are discovered
 10, 000 are synthesized each year
 compare to inorganic compound (1.7 million)
9
 approximately 85% known compounds are organic
Can bond with another Carbon
O Catenation is the linkage of atoms of the same element into longer chains.
Form of Allotropes
 the property of some chemical elements to exist in two or more different forms
 Carbon is capable of forming many allotropes due to its valency.
O Diamond – the hardest known natural mineral
- Each carbon atom in a diamond is covalently bonded to four other carbons in a
tetrahedron
O Graphite – named by Abraham Gottlob Werner in 1789, from the Greek (graphein, "to
draw/write", for its use in pencils)
- an electrical conductor
O Lonsdaleite – named in honour of Kathleen Lonsdale
- also called hexagonal diamond in reference to the crystal structure
- it forms when meteorites containing graphite strike the Earth
 Many more allotropes and forms of carbon have been discovered and researched including
ball shapes such as buckminsterfullerene and sheets such as graphene
O Buckminsterfullerene – discovered in 1985 by a team of scientists from Rice University and
the University of Sussex
- Richard Buckminster "Bucky" Fuller
- in April 2003, fullerenes were under study for potential medicinal use
 Larger scale structures of carbon include nanotubes, nanobuds and nanoribbons.
 Other unusual forms of carbon exist at very high temperature or extreme pressures
Essential in understanding biochemistry

O biochemicals, including carbohydrates, lipids, proteins, enzymes, nucleic acids (DNA and RNA),
hormones, vitamins, and almost all other important chemicals in living systems are organic
compounds
Organic compounds differ from inorganic compounds in many of their properties

Organic Compounds Inorganic Compounds
 Bonding is almost entirely covalent
 Most have ionic bond
 May be gases, liquids, or solids with low
 Most are solids with high melting points
melting points (less than 360°C)
 Many are soluble in water
 Most are soluble in organic solvents
 Almost all are insoluble in organic solvents
 Aqueous solution do not conduct
 Aqueous solution conduct electricity
electricity
 Very few burn
 Almost all burn
 Reactions are often very fast
 Reactions are usually slow
10
1.2 WHERE DO WE OBTAIN ORGANIC COMPOUNDS?
Isolation from nature

o living organisms are “chemical factories”
o one way to get organic compounds – extract, isolate, and purify – from biological sources
o example: RUBBER
Synthesis in the laboratory

o compounds made in the laboratory are identical in both physical and chemical
properties to those found in nature – 100%
LESSON 2 The Carbon Atom and its C–C Bond

 Bonding is the joining of two atoms in a stable arrangement.
o Bonding may occur between atoms of the same or different elements.
 General rules governing the bonding process.
o Through bonding, atoms attain a complete outer shell of valence electrons.
o Through bonding, atoms attain a stable noble gas configuration of electrons.
o Ionic bonds result from the transfer of electrons from one element to another.
o Covalent bonds result from the sharing of electrons between two nuclei.
How many covalent bonds will a particular atom typically form?

• Atoms with one, two, three, or four valence electrons form one, two, three, or four bonds,
respectively, in neutral molecules.
• Atoms with five or more valence electrons form enough bonds to give an octet. This results
in the following simple equation:
2.1 HYBRIDIZATION
Valence Bond Theory
 a covalent bond forms when two atom approach each other closely so that a singly occupied
orbital on one atom overlaps a singly occupied orbital on the other atom
 example: H2 -- H : H
 H – H bond are formed by head-on overlap of two atomic orbitals called sigma (σ) bonds.
Single Bond
O a  bond concentrates electron density on the axis that joins two nuclei
O all single bonds are  bonds
O carbon has two core electrons, plus four valence electrons
O this lowest energy arrangement of electrons for an atom is called its ground state 11
O carbon should form only two bonds because it has only two unpaired valence electrons, and CH2
should be a stable molecule
O promotion of an electron from a 2s to a vacant 2p orbital would form four unpaired electrons for
bonding
O this process requires energy because it moves an electron to a higher energy orbital
O this higher energy electron configuration is called an electronically excited state
o This description is still not adequate

– chemists have proposed that atoms like carbon do not use pure s and pure p orbitals
in forming bonds
– atoms use a set of new orbitals called hybrid orbitals
O Hybridization is the combination of two or more atomic orbitals to form the same number of hybrid
orbitals, each having the same shape and energy.
o Hybridization occurs to minimize electron pair repulsions when atoms are brought together
to form molecules.
o Each of these hybridzation schemes corresponds to one of the five fundamental VSEPR
geometries.
sp3 Hybridization
– Hybridization of one 2s orbital and three 2p orbitals for carbon forms four hybrid
orbitals, each with one electron.
12
sp2 Hybridization
sp Hybridization
13
2.2 LEWIS STRUCTURE
 are electron dot representations

for molecules
 there are three general rules for
drawing Lewis structures
1. Draw only the valence
electrons.
2. Give every second-row
element no more than
eight electrons.
3. Give each hydrogen two electrons.
2.3 DETERMINING MOLECULAR SHAPE
Bond Length
- the average distance between the centers of two bonded nuclei.
O Bond lengths are typically reported in picometers (pm), where 1 pm =10–12 m.
O Bond length decreases across a row of the periodic table as the size of the atom decreases.
O Bond length increases down a column of the periodic table as the size of an atom increases.
Average bond length:
14
Bond Angle
 determines the shape around any atom
bonded to two other atoms
 The most stable arrangement keeps
these groups as far away from each
other as possible.
Three-dimensional Geometry
 A solid line is used for a bond in the plane.
 A wedge is used for a bond in
front of the plane.
 A dashed line is used for a
bond behind the plane.
2.4 DRAWING ORGANIC STRUCTURE
Condense Structure
 All of the atoms are drawn in, but the two-electron bond lines are generally omitted.
 Atoms are usually drawn next to the atoms to which they are bonded.
 Parentheses are used around similar groups bonded to the same atom.
 Lone pairs are omitted.
Skeletal Structure
O Assume there is a carbon atom at
the junction of any two lines or at
the end of any line.
O Assume there are enough
hydrogens around each carbon to
make it tetravalent.
15
Line Bond Structure
O Draw in all carbon, heteroatoms and the hydrogens directly bonded to them.
2.5 ISOMERS
There is no simple way of predicting how
many isomers a given molecular formula will yield (it
can range from one to many).
• In drawing a Lewis structure for a molecule with
several atoms, sometimes more than one
arrangement of atoms is possible for a given
molecular formula.
• For example, there are two acceptable arrangements of atoms for the molecular formula C2H6O.
• Isomers are different molecules having the same molecular formula
Types of Isomers
1. Constitutional isomers
– have the same molecular formula, but the connectivity of their atoms is different
2. Stereoisomer
– have the same order and types bonds but different spatial arrangement; with different
properties
– Many biological important chemicals, like sugars, exist as stereoisomers
• Below are the possible combinations of C having a total of four bonds.
16
In a hydrocarbon where all the C atoms have only single bonds and no rings are involved, the
compound would have the maximum number of H atoms. If any of the bonds are replaced with
double or triple bonds, or if rings are involved, there would be a “deficiency” of H atoms.
By calculating the index of hydrogen deficiency (IHD), we can tell from the molecular formula
whether and how many multiple bonds and rings are involved.
2.5.2 Index of Hydrogen Deficiency (IHD) also called the Degree of Unsaturation
 A double bond and ring each counts as one IHD.
 A triple bond counts as two IHD.
 O and S atoms do not affect the IHD.
 Halogens (F, Cl, Br, I) are treated like H atoms
 For each N, add one to the number of C and one to the number H
o (CH5N is treated as C2H6. CH4N2O is treated as C3H6 by adding 2 to # of C and 2 to
# of H).
Formula: Hydrocarbons (CxHy): IHD = ( ) where x and y stand for # of C and H
Example: IHD for C2H4 is (2(2) + 2 - 4)/2 = 1

This means it can have either one double bond or one ring. It cannot have a triple bond.
Since you cannot form a ring with only two C’s, it must have a double bond.
References
Books:
th
Brown, W. & Poon, T. (2014). Organic Chemistry, 5 Edition. USA: Cengage Learning
th
Brown, W., Iverson, B., Anslyn, E., & Foote, C. (2018). Organic Chemistry, 8 Ed. USA: Cengage Learning
nd
Bruice, P. (2014). Essential Organic Chemistry, 2 Edition. USA: Pearson Education Limited
nd
Bruice, P. (2016). Organic Chemistry, 2 Edition. USA: Pearson Education Limited
th
Carey, F. & Giuliano, R. (2014). Organic Chemistry, 9 Edition. USA: McGraw-Hill Companies, Inc.
nd
Klein, David. (2016). Organic Chemistry As A Second Language, 2 Edition. USA: John Wiley & Sons, Inc.
th
McMurray, J. (2016). Organic Chemistry, 9 Edition. USA: Cengage Learning.
nd
McMurray, J., (2015). Organic Chemistry with Biological Application. 2 Edition. USA: Cengage Learning.
rd
Smith, Janice. (2011). Organic Chemistry, 3 Edition. USA: McGraw-Hill Companies, Inc.
th
Vollhardt, P. & Schore, N. (2014). Organic Chemistry: Structure and Function, 7 Edition. USA: W.H.
Freeman and Company
Internet:
About.com Chemistry.2013.Retrieved from http://chemistry.about.com/library/weekly/ aa062703a.htm
Daley, Richard F. and Daley, Sally J.2005.Retrieved from http://www.ochem4free.info/ YQcr3l7Abrssp/02-Naming.pdf
Functional Group.Retrieved from http://www.as.utexas.edu/astronomy/education/
spring07/scalo/secure/AbioFunctionalGrpsVollIRspect.pdf
Organic chemistry Portal. Retrieved from http://www.organic-chemistry.org/ 17
Reusch, William. 2010. Virtual Textbook of Organic Chemistry.Retrieved from
http://www2.chemistry.msu.edu/faculty/reusch/VirtTxtJml/intro1.htm
UC Davis ChemWiki by University of California, Davis.2010 Retrieved from
http://chemwiki.ucdavis.edu/Organic_Chemistry
18
PROBLEM SET
1. Identify the hybridization of each carbon below.

5 6
1 2 3 C C 1. _______________ 5._____ __________
C C C C4 2. _______________ 6._______________
C C 3. _______________ 7._______________
7 8 4. _______________ 8._______________
2. Identify how many sigma (σ) or pi (π) bonds are present in the following structure (ignore the
arrows).
a. b.
3. Draw one valid Lewis structure for each compound. Assume that the atoms are arranged as drawn.
a. b.
4. Complete the following structural formulas by adding enough hydrogens to complete the
tetravalence of each carbon. Then write the molecular formula of each compound.
a. b. c.
5. Convert each molecule into a skeletal structure.

a.
19
6. Convert the following skeletal structure to line bond structure .
_____________________________________________
____________________________________________
7. Simplify each condensed structure by using parentheses around similar groups.
a. c. _____________
___________________
b. ________________ d.
____________________________________
8. Calculate the IHD for each of the following.
a. b.
20
No part of this module may be reproduced, stored in a retrieval system or transmitted in any form or by any means, mechanical,
electronic, photocopying, recording or otherwise without the prior written permission of the author/s.
Chapter Organic Molecules and It’s Functional Group
Objectives
1. Identify and describe the characteristic features of an organic compound.
2. Familirize with the different functional groups found in organic molecules.
3. Determine the properties of an organic compound.
4. Use the properties of organic molecules to explain some basic biological phenomena.
LESSON 1 The Functional Groups
What are the characteristic features of an organic compound?

 Heteroatoms—atoms other than carbon or hydrogen.
o Common heteroatoms are nitrogen, oxygen, sulfur, phosphorus, and the halogens.
  Bonds. The most common π bonds occur in C – C and C – O double bonds.
1.1 FUNCTIONAL GROUP

 an atom or a group of atoms with characteristic chemical and physical properties
 the reactive part of the molecule
We can subdivide the most common functional groups into three types. A more complete list of
functional groups is presented on the inside front cover.
• Hydrocarbons
• Compounds containing a C – Z  bond where Z = an electronegative element
• Compounds containing a C=O group
Hydrocarbon
 are compounds made up of only the elements carbon and hydrogen
 may be aliphatic or aromatic.
[1] Aliphatic hydrocarbons – can be divided into three subgroups
o Alkanes have only C – C σ bonds and no functional group.
o Alkenes have a C – C double bond as a functional group.
o Alkynes have a C – C triple bond as a functional group.
[2] Aromatic hydrocarbons. This class of hydrocarbons was so named because many of the
earliest known aromatic compounds had strong, characteristic odors.
21
Table 3.1 Functional Groups
22
LESSON 2: Physical Properties
 The strength of a compound’s intermolecular forces determines many of its physical properties,
including its boiling point, melting point, and solubility.
 Intermolecular forces are the interactions that exist between molecules.
 A functional group determines the type and strength of these interactions.
2.1 BOILING POINT (BP)
 the temperature at which a liquid is

converted to a gas
 The stronger the intermolecular
forces, the higher the boiling point
 Example:
 The larger the surface area, the higher the boiling point.
 The more polarizable the atoms, the higher the boiling point.
MELTING POINT (MP)

 the temperature at which a solid is converted to its liquid phase
 The stronger the intermolecular forces, the higher the melting point.
 Given the same functional group, the more symmetrical the compound, the higher the melting
point.
23
Example:
Symmetry also plays a role in determining the melting points of compounds having the same
functional group and similar molecular weights, but very different shapes
Example:
2.6 SOLUBILITY
 the extent to which a compound, called the solute,
o dissolves in a liquid, called the solvent
 Compounds dissolve in solvents having similar kinds of intermolecular forces.
 “Like dissolves like.”
 Polar compounds dissolve in polar solvents. Nonpolar or weakly polar compounds
o dissolve in nonpolar or weakly polar solvents.
References
Books:
th
th
nd
nd
th
nd
th
nd
rd
th
Freeman and Company
Internet:
Organic chemistry Portal. Retrieved from http://www.organic-chemistry.org/
Reusch, William. 2010. Virtual Textbook of Organic Chemistry.Retrieved from 24
PROBLEM SET
1. Identify the different functional group, by encircling, present on the following organic compound
below:
2. Draw the structure of a compound fitting each description:
a. An aldehyde with molecular formula C4H8O

b. A carboxylic acid with molecular formula C4H8O2
a. A ketone with molecular formula C4H8O
b. d. An ester with molecular formula C4H8O2
25
3. Which compound in each pair has the higher boiling point?
4. Intramolecular forces of attraction are often important in holding large molecules together. For
example, some proteins fold into compact shapes, held together by attractive forces between nearby
functional groups. A schematic of a folded protein is drawn here, with the protein backbone indicated
by a blue-green ribbon, and various appendages drawn dangling from the chain. What types of
intramolecular forces occur at each labeled site (A–F)?
A: ____________________________ D: ____________________________
B: ____________________________ E: ____________________________
C: ____________________________ F: ____________________________
26
Chapter 3 Alkane
Objectives
1. Understand the IUPAC System of naming organic substances
2. Apply IUPAC System in naming organic alkane
3. Familiarize with some of the alkanes found around us
4. Examine and distinguish the different physical and chemical properties of
alkanes
5. Identify and draw the different conformation of acyclic and cyclic alkanes
LESSON 1 IUPAC System of Nomenclature
Carbon atoms in alkanes and other organic compounds are classified by the number of other
carbons directly bonded to them.
• A primary carbon (1° carbon) is bonded to one other C atom.

• A secondary carbon (2° carbon) is bonded to two other C atoms.
• A tertiary carbon (3° carbon) is bonded to three other C atoms.
• A quaternary carbon (4° carbon) is bonded to four other C atoms.
Naming organic compounds has become big business for drug companies. The IUPAC name of an
organic compound can be long and complex, and may be comprehensible only to a chemist. As a
result, most drugs have three names:
 Systematic: The systematic name follows the accepted rules of nomenclature and indicates the
compound’s chemical structure; this is the IUPAC name.
 Generic: The generic name is the offi cial, internationally approved name for the drug.
 Trade: The trade name for a drug is assigned by the company that manufactures it. Trade names
are often “catchy” and easy to remember. Companies hope that the public will continue to
purchase a drug with an easily recalled trade name long after a cheaper generic version becomes
available.
27
The system of nomenclature is devised by the International Union of Pure and Applied Chemistry
(IUPAC, usually spoken as eye-you-pac).
– Has three parts: prefix, parent, and suffix
Prefix — Parent — Suffix
Where are the substituents? How many carbons? What family-functional group?
• The parent name indicates the number of carbons in the longest continuous carbon chain in
the molecule.
• The suffix indicates what functional group is present.
• The prefix reveals the identity, location, and number of substituents attached to the carbon
chain.
LESSON 2: Naming of ALKANE
• for the simple n-alkanes consist of the parent name, which indicates the number of carbon
atoms in the longest carbon chain, and the suffix —ane
• The parent name for one carbon is meth-, for two carbons is eth-, and so on
Naming Substituents
o Carbon substituents bonded to a long carbon chain are called alkyl groups.
• An alkyl group is formed by removing one hydrogen from an alkane
o To name an alkyl group, change the -ane ending of the parent alkane to -yl.
• methane (CH4) becomes methyl (CH3 – )
• ethane (CH3CH3) becomes ethyl (CH3CH2 – )
o Naming three- and four-carbon alkyl groups is more complicated because the parent hydrocarbons 28
have more than one type of hydrogen atom.
o For example, propane has both 1° and 2° H
atoms, and removal of each of these H
atoms forms a different alkyl group with a
different name, propyl or isopropyl.
 there are four possible

alkyl groups containing
four carbon atoms, each
having a different name:
butyl, sec-butyl, isobutyl,
and tert-butyl
HOW TO NAME AN ACYCLIC ALKANE USING THE IUPAC SYSTEM
Step 1) Find the parent carbon chain and

add the suffix.
Step 2) Number the atoms in the carbon chain.

• Number the longest chain to give the first
substituent the lower number.
• If the first substituent is the same distance

from both ends, number the chain to give the
second substituent the lower number.
29
• When numbering a carbon chain results in the same numbers from either end of the chain, assign
the lower number alphabetically to the first substituent.
Step 3) Name and number the substituents.
• If two or more identical substituents are bonded to the longest chain, use prefixes to indicate
how many: di- for two groups, tri- for three groups, tetra- for four groups, and so forth.
Step 4) Combine substituent names and numbers + parent + suffix.
HOW TO NAME AN CYCLIC ALKANE OR CYCLOALKANE USING THE IUPAC SYSTEM
Step 1) Find the parent cycloalkane.

• Count the number of carbon atoms in the ring and use the parent name for that number of carbons.
• Add the prefix cyclo- and the suffix -ane to the parent name. 30
Step 2) Name and number the substituents.
• For rings with more than one
substituent, begin numbering at one
substituent and proceed around the ring
clockwise or counter-clockwise to give
the second substituent the lower
number.
• With two different substituents, number

the ring to assign the lower number to
the substituents alphabetically.
LESSON 3 Alkanes Around Us
The simplest family of molecules—the alkanes—are aliphatic hydrocarbons having only C – C and C – H
(sigma) bonds.
 Alkanes are often described as saturated hydrocarbons: hydrocarbons because they contain only
carbon and hydrogen
o saturated because they have only C – C and C – H single bonds and thus contain the
maximum possible number of hydrogen per carbon
 occasionally called aliphatic compounds, a name derived from the Greek aleiphas, meaning “fat”
 can be categorized as acyclic or cyclic
o Acyclic alkanes have the molecular formula CnH2n + 2 (where n = an integer) and contain
only linear and branched chains of carbon atoms.
o Cycloalkanes contain carbons joined in one or more rings. Because their general formula
is CnH2n, they have two fewer H atoms than an acyclic alkane with the same number of
carbons
31
 small portion of the atmospheres of the outer gas planets contains alkane compounds
– such as Jupiter, Saturn, Uranus and Neptune, also in Titan, a satellite of Saturn
 Natural gas contains primarily methane and ethane, with some propane and butane
– Produced primarily by organisms such as Archaea, found for example in the gut of
cows
1. Methane, CH4
 the principal component of natural gas, which contains from 50 to 90% methane
 Burning methane in the presence of oxygen produces carbon dioxide and water.
CH4 + O2  CO2 + H2O
 flammable only over a narrow range of concentrations (5–15%) in air
 a potent greenhouse gas and also affects the degradation of the ozone layer
 also an asphyxiant and may displace oxygen in an enclosed space
2. Ethane, C2H6
 a colorless, odorless, flammable gas
 isolated on an industrial scale from natural gas
 a greenhouse gas that occurs as a trace gas in the Earth's atmosphere
 detected as a trace component in the atmospheres of all four giant planets, and in the
atmosphere of Saturn's moon Titan
 a cryogenic liquid which liquefied gas at very low temperature
3. Propane, C3H8
 normally a gas, but compressible to a transportable liquid
 commonly known as liquefied petroleum gas (LPG or LP gas)
 Nontoxic; however, when abused as an inhalant it poses a mild asphyxiation risk through
oxygen deprivation
4. Butane, C4H10
 an alkane with four carbon atoms
 highly flammable, colorless, easily liquefied gases
 blended with propane and other hydrocarbons, it is referred to commercially as LPG
5. Pentane, C5H12
 are components of some fuels and are employed as specialty solvents in the laboratory
 one of the primary blowing agents used in the production of polystyrene foam
6. Hexane, C6H14
 significant constituents of gasoline
 colorless liquids at room temperature with boiling points between 50 and 70 °C
 used in the formulation of glues for shoes, leather products, and roofing
 Inhalation of high concentrations produces first a state of mild euphoria, followed by
headaches and nausea
7. Heptane, C7H16
 undesirable in petrol, because it burns explosively, causing engine knocking 32
o used as a test fuel component in anti-knock test engines
 commercially available as mixed isomers for use in paints and coatings
8. Octane, C8H18
 are very flammable and a component of gasoline (petrol)
 "high octane" levels in their gasoline in advertisements refer to the octane rating, which is
a measure for the anti-knocking properties of gasoline
o Octane rating or octane number is a standard measure of the performance of a motor
or aviation fuel – a measure of the fuel's tendency to burn in a controlled manner, rather
than exploding in an uncontrolled manner
9. Decane, C10H22
 one of the component of gasoline
Ecological relationship between the sand bee and the early spider orchid
• Sand bees use pheromones in order to identify a mate
• the females emit a mixture of tricosane (C23H48), pentacosane (C25H52) and heptacosane (C27H56) in
the ratio 3:3:1
• males are attracted by specifically this odor
• Early Spider Orchid flower not only resemble the appearance of sand bees, but also produce large
quantities of the three alkanes in the same ratio as female sand beesit allows the orchid to
transfer its pollen
Biologically active alkane (Wax/Lipids)
 Saturated Fat/oil
– have no double bonds between the carbon atoms of the fatty acid chain and are thus
fully saturated with hydrogen atoms
– Example: Stearic acid
FOSSIL FUELS
Many alkanes occur in nature, primarily in natural gas and petroleum. Both of these fossil fuels
serve as energy sources, formed from the degradation of organic material long ago.
O Natural gas is composed largely of methane (60% to 80% depending on its source), with lesser
amounts of ethane, propane, and butane.
o these organic compounds burn in the presence of oxygen, releasing energy for cooking and
heating.
O Petroleum is a complex mixture of compounds, most of which are hydrocarbons containing 1–40
carbon atoms.
o Distilling crude petroleum, a process called refining, separates it into usable fractions that
differ in boiling point.
o Most products of petroleum refining provide fuel for home heating, automobiles, diesel
engines, and airplanes.
o Each fuel type has a different composition of hydrocarbons:
 gasoline: C5H12 – C12H26
 kerosene: C12H26 – C16H34
 diesel fuel: C15H32 –C18H38 33
o Petroleum provides more than fuel. About 3% of crude oil is used to make plastics and other
synthetic compounds including drugs, fabrics, dyes, and pesticides.
LESSON 4 Physical and Chemical Properties of Alkanes
Alkanes are sometimes referred to as paraffins, a word derived from the Latin parum affinis,
meaning “little affinity.”
• show little chemical affinity for other substances and are chemically inert to most laboratory
reagents
• contain only nonpolar C – C and C – H bonds, and as a result they exhibit only weak van der Waals
forces
• also relatively inert biologically and are not often involved in the chemistry of living organisms
BOILING POINT
• have low bp’s compared to more polar compounds of comparable size
• Bp increases as the number of carbons increases because of increased surface area.
• Bp of isomers decreases with branching because of decreased surface area.
MELTING POINT
• have low mp’s compared to more polar compounds of comparable size.
• Mp increases as the number of carbons increases because of increased surface area
• Mp increases with increased symmetry.
SOLUBILITY: A CASE OF “LIKE DISSOLVES LIKE”

• Alkanes are soluble in organic solvents. An example of “like dissolves like”
• such as toluene and diethyl ether
• Alkanes are insoluble in water they cannot form hydrogen bonds with water
DENSITY
• The average density of the liquid alkanes is about0.7 g/mL; that of higher-molecular-weight
alkanes is about 0.8 g/mL.
• liquid and solid alkanes are less dense than water (1.000 g/mL), and because they are insoluble
in water, they float on water
REACTIONS OF ALKANES
Alkanes are the only family of organic molecules that have no functional group, and
therefore, alkanes undergo few reactions
• Alkanes react with oxygen, halogens, and a few other substances under appropriate conditions
 Combustion/Redox Reaction: Reaction with oxygen occurs in an engine or furnace when
the alkane is used as a fuel.
 Example: CH4 + 2 O2 → CO2 + 2 H2O + 890 kJ/mol (213 kcal/mol)
34
 Radical Substitution
 Substitution of R-H by -X provides the alkyl
halide, R-X and HX.
 Alkane R-H relative reactivity order :
3o > 2o > 1o > methyl
 Halogen reactivity: F2 > Cl2 > Br2 > I2
 Only chlorination and bromination are useful in the laboratory.
 Reaction proceeds
via a radical chain
mechanism
References
Books:
th
th
nd
nd
th
nd
th
nd
rd
th
Freeman and Company
Internet:
Organic chemistry Portal. Retrieved from http://www.organic-chemistry.org/
Reusch, William. 2010. Virtual Textbook of Organic Chemistry.Retrieved from 35
36
PROBLEM SET
Name____________________________ Program/Year/Section____________ Date______________
1. Give the IUPAC name for each compound.
a. _________________________ d. _________________________
b. _________________________ e. _________________________
c. _________________________ f. _________________________
2. Give the structure corresponding to each IUPAC name.
a. 3-methylhexane c. 3,5,5-trimethyloctane e. 3-ethyl-5-isobutylnonane

b. 3,3-dimethylpentane d. 3-ethyl-4-methylhexane
37
3. Give the IUPAC name for each compound.
a. ___________________________ d. ___________________________
b. ___________________________ e. ___________________________
c. ___________________________ f. ___________________________
4. Give the structure corresponding to each IUPAC name.
a. 1,2-dimethylcyclobutane d. 1-sec-butyl-3-isopropylcyclopentane
b. 1,1,2-trimethylcyclopropane e. 1,1,2,3,4-pentamethylcycloheptane
c. 4-ethyl-1,2-dimethylcyclohexane
38
5. The melting points and boiling points of two isomeric alkanes are as follows: CH 3(CH2)6CH3, mp = –57
°C and bp = 126 °C; (CH3)3CC(CH3)3, mp = 102 °C and bp = 106 °C.
(a) Explain why one isomer has a lower melting point but higher boiling point.
(b) Explain why there is a small difference in the boiling points of the two compounds, but a huge
difference in their melting points.
6. Draw the products of each combustion reaction.
7. Name and draw structural formulas for all possible monochlorination products that might be formed
in each reaction.
39
40
41
THE COMPILER
A faculty, Science Laboratory In-Charge, the BioSA
Adviser, BS Bio Extension CHiar, and PTCA Adviser of the
School of Arts and Sciences of Aklan State University. A
registered Professional Teacher; taught different area in
Chemistry, Biology, Physics, Earth Science, and
Professional Education subjects for more than 14 years.
Graduated Cum Laude at Philippine Normal University
with a degree of Bachelor of Science in Chemistry for
Teachers, finished Master in Chemistry at De La Salle
University, Manila, and currently taking Doctor of
Education in Science Education at Filamer Christian
University, Roxas City, Capiz.

Banga, Aklan
V ision:
An Academic Pillar of Excellence (APEX)
for sustainable development.
M ission:
Aklan State University is committed to offer degree and non-
degree curricula in agriculture, forestry, veterinary medicine, fishery,
arts and sciences, engineering and technology, education and
management science to produce globally competent professionals, leaders,
and entrepreneurs through technological breakthrough in research,
efficacy of extension and efficacy in production. 42

Module in Organic Chemistry: Aklan State University

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The volume 1 of this module is divided into three chapters,

The compiler of this module is excited to bring you an ever-expanding

Chapter 1 Introduction to Organic Chemistry

Lesson 1 What is Organic Chemistry? 9

Chapter 2 Organic Molecules and It’s Functional Group

Lesson 2 Physical Properties 23

Lesson 1 IUPAC System of Nomenclature 27

Lesson 3 Alkanes Around Us 31

Writing and Naming Chemical Formula

1.1 WRITING CHEMICAL FORMULAS

Formulas of Binary Ionic Compounds

Potassium and Sulfur

Formulas of Ternary Ionic Compounds

For example: Potassium and sulfate ion

Common Polyatomic Ions

The Stock Method of Naming

The Old, Classic, or Common Way of Naming

Rules for Naming Molecular Compounds:

Examples of Molecular Compound Names:

1.3 NAMING ACIDS, BASES, AND HYDRATES

Name____________________________ Course/Year/Section____________ Date______________

1. Write chemical formulas for the compounds in each box

2. Write the formulas for the following compounds:

3. Give the correct IUPAC name of the following chemical formula

LESSON 1 What is Organic Chemistry?

1.1 WHAT’S SO SPECIAL ABOUT CARBON?

Number of Organic Compounds

Essential in understanding biochemistry

Organic compounds differ from inorganic compounds in many of their properties

Isolation from nature

Synthesis in the laboratory

LESSON 2 The Carbon Atom and its C–C Bond

How many covalent bonds will a particular atom typically form?

o This description is still not adequate

 are electron dot representations

2.3 DETERMINING MOLECULAR SHAPE

Average bond length:

2.4 DRAWING ORGANIC STRUCTURE

• Below are the possible combinations of C having a total of four bonds.

Example: IHD for C2H4 is (2(2) + 2 - 4)/2 = 1

Name____________________________ Course/Year/Section____________ Date______________

1. Identify the hybridization of each carbon below.

5. Convert each molecule into a skeletal structure.

7. Simplify each condensed structure by using parentheses around similar groups.

8. Calculate the IHD for each of the following.

LESSON 1 The Functional Groups

What are the characteristic features of an organic compound?

1.1 FUNCTIONAL GROUP

2.1 BOILING POINT (BP)

 the temperature at which a liquid is

MELTING POINT (MP)

2. Draw the structure of a compound fitting each description:

a. An aldehyde with molecular formula C4H8O

LESSON 1 IUPAC System of Nomenclature

• A primary carbon (1° carbon) is bonded to one other C atom.

Prefix — Parent — Suffix

LESSON 2: Naming of ALKANE

 there are four possible

HOW TO NAME AN ACYCLIC ALKANE USING THE IUPAC SYSTEM

Name______________ Course/Year/Section Date

Name______________ Course/Year/Section Date