Agri 114

Organic Chemistry

1. Title of the Module

Chapter 1: Introduction to Organic Chemistry and Review of Some Basic Concepts in
General Chemistry
2. Introduction
Organic chemistry studies the structure, properties and reactions of organic compounds,
which contain carbon in covalent bonding. The study of structure determines their chemical
composition and formula and the study of properties includes physical and chemical properties, and
evaluation of chemical reactivity to understand their behavior. The study of organic reactions
includes the chemical synthesis of natural products, drugs, and polymers, and study of individual
organic molecules in the laboratory and via theoretical (in silico) study.

3. Learning Outcome
After studying the module the student are expected to:
a. know the history of the development of organic chemistry
b. relate the usefulness of organic chemistry to everyday life
c. review basic concepts on atoms and Periodic Table

4. Learning Content
Topic 1. History ad Development of Organic Chemistry
 Mid 1700 – Alchemists noticed unexplained differences between compounds derived from living
sources and those obtained from minerals
 1770 – Torbern Bergman – a Swedish chemist expressed the difference between compounds from
living organisms (as organic) and compounds from minerals (as inorganic)
 The term Organic Chemistry was born which soon came to mean as chemistry of compounds
from living organisms.
 19th century – Vital Force theory

 Scientists believed that only living organisms had the vital force necessary to produce organic
compounds. The believed that organic compounds have undefinable vital force as a result of their
origin in living sources
 1828 – Friedrich Wohler dispelled the vital force theory when he synthesized the organic
substance urea from inorganic compounds lead cyanate and ammonium hydroxide
 1859 –The first oil-producing well was drilled which opened up an endless possibilities for
organic compounds
  Mid 1800s –The Vitalistic theory ended since it had become clear that all compounds can be
applied with the same basic scientific principles.
 They concluded that the basic difference between organic and inorganic compounds is the
presence of CARBON

Organic Chemistry is defined as study of Carbon and its compounds

 Organic compound consists primarily of Carbon and Hydrogen but may contain other elements
such as N, O, P, Si, S, and the halogens

What’s Special About Carbon? Why devote a branch of chemistry for the study of the
compounds of a single element?
 Life on earth is based on the element Carbon which is essential to life

 Carbon can form 4 strong covalent bonds and can bond with one another forming long chains and
rings, thus there are more than several millions of known organic compounds
 The uses and occurrences of carbon compounds are virtually limitless and in many cases essential
to life in this planet.

Topic 2. Applications of Organic Chemistry

Most of the things around us are made up of carbon compounds namely:
1. Foodstuffs like carbohydrates, fats and proteins, as well as food additives and preservatives
2. Organs, tissues and cells of organisms are constructed using carbon and carbon compounds.
Stored energy in living organism are also in the form of carbon compounds
3. Petroleum used in industrial activities and are refined as gasoline, LPG gas and more.
4. Plastics like polyvinyl chloride (PVC), styrofoam, polyethylene, teflon, and the like
5. Natural and synthetic fibers like cotton, silk, nylon, polyesters, etc
6. Drugs and medicines like aspirin, decongestants, etc.
7. Hygienic and beauty products like soap, detergents, disinfectants, deodorizer, perfumes and
cosmetics
8. Agricultural chemicals
9. Paints and dyes

Topic 2. Review of Some Basic Concepts in General Chemistry

Atomic Structure
Atom – the smallest portion of an element that retains all the properties of the element.
The atoms of one element differ from those of other elements, and so give characteristic properties of
each element.
 3 fundamental particles of an atom:
1. Proton (p+) – positively charged particles located inside the nucleus of an atom with a mass of
approximately 1 amu (atomic mass unit)
2. Neutrons (n) – no charge or neutral particles located inside the nucleus of an atom with a mass or
weight of approximately 1 amu
3. Electrons (e-) – negatively charged particles located outside the nucleus of an atom
with a mass or weight of 1/1837 amu

Fig.1.Bohr’s Model of
an Atom

Atomic number
▫ Each element is given an atomic number that represents that element.
▫ It Indicates the number of protons in the nucleus of an atom.
 ▫ It is equal to the number of electrons since all atoms are electrically neutral.

Atomic Mass or Mass number = Number of protons + Number of neutrons

Number of Neutrons = Mass number ̶ Number of protons
Practically, all mass of the atom is located in its nucleus because the mass of the electrons is negligible
compared to the masses of both protons and neutrons.

Example 1 :
In the Periodic Table, Carbon has atomic No. of 6 and Atomic Mass of 12
– This means that it also has 6 protons and 6 electrons. In an atom the positive and negative
charge should be equal because it is supposed to be neutral.
If the Mass No is 12 and the number of protons is 6 then the number of neutrons is equal to 6.
Ex. 2. Chlorine has an atomic no of 17.
a) How many protons does it have? ____
b) How many electrons does it have? ____
c) If the mass number is 35, how many neutrons does it have? ____

Answer: a. 17 b. 17 c. 18

Atomic Orbitals

Electrons move along paths called atomic orbitals, or subshells. There are several different orbital shapes
—s, p, d, and f—but we will be focusing mainly on s and p orbitals for now.
1st energy level contains only one s orbital -
2nd energy level contains one s orbital and three p orbitals
3rd energy level contains one s orbital, three p orbitals, and five d orbitals.
Each orbital can contain a maximum of 2 electrons
Therefore the maximum number of e-s for each orbital:
s =2 p=6 d=10 f=14
Electronic configuration of an element?
An electron configuration describes the distribution of electrons among atomic orbitals in the atom
Two general methods used to denote electron configurations
1. Subshell (sublevel) notation- uses numbers to designate the principal energy levels or principal shells
and the letters s,p,d,f to identify the sublevels. A superscript number following the letter indicates the
number of electrons in the designated subshell.
Proper order is: 1s, 2s, 2p, 3s,3p,4s, 3d, 4p,5s, 4d, 5p,6s, 4f,5d, 6p,
7s,5f,6 d,7p

The Madelung energy ordering rule:

Example 1:
For an atom having an atomic number of 7, the electron configuration is written
1s22s22p3
Example 2
Li – The atomic number of Li is 3, therefore the number of electrons is also 3
Li3 - 1s22s1 F9 - 1s22s22p5
C6 - 1s22s22p2

2. Orbital Diagram – shows how the electrons are distributed in the subshells or sublevels. It uses boxes
to represent an orbital and arrows to represent electrons found in the orbitals. The direction of the
arrows indicates the direction of the spins.

Example:
For an atom having an atomic number of 7, the electron configuration is drawn as

3. Noble gas core abbreviated subshell notation- The inner core electron configuration is represented
by a noble gas that have the same configuration. The subshell configuration of the valence electron is
shown after the symbol for the noble gas.

Example:
For an atom having an atomic number of 12, the electron configuration is writtern
1s22s22p63s2
Since the electron configuration of argon is 1s22s22p6, the electron configuration of the atom
can be written as
[Ar] 3s2
Procedure in writing electron configuration
1. Using Periodic table find the atomic number for the element
2. Distribute the number of electrons in the various subshells according to the order of filling of orbitals
given above.
3. Do not exceed the maximum no. Of electrons for any orbital or for any subshell, two electrons in the
same orbital must have opposite spin.
4. In an orbital diaagrams, be sure that when a subshell is partly filled, orbitals in that subshell are singly
occupied by electrons having parallel spins.

Sample Problem

Write the electronic configuration of phosphorus using the subshell notation, orbital diagram and the
noble gas abbreviated notation
Answer:
From periodic table , atomic number of P = 15
Subshell notation = 1s22s22p63s23p3
noble gas abbreviated notation = [Ar] 3s23p3
orbital diagram

1s 2s 2p 3s 3p

Topic 2. Periodic Table

The Periodic Table, also known as the periodic table of elements, is a tabular display of the chemical
elements, which are arranged by atomic number, electron configuration, and recurring chemical
properties. The structure of the table shows periodic trends. The seven rows of the table, called periods,
generally have metals on the left and nonmetals on the right. The columns, called groups, contain
elements with similar chemical behaviors. Six groups have accepted names as well as assigned numbers:
for example, Group VIIA (column 17) elements are the halogens; and Group VIII or Group 0 (column
8) are the noble gases. Also displayed are four simple rectangular areas or blocks associated with the
filling of different atomic orbitals.
The elements from atomic numbers 1 (hydrogen) through 118 (oganesson) have all been discovered or
synthesized, completing seven full rows of the periodic table. The first 94 elements, hydrogen
through plutonium, all occur naturally, though some are found only in trace amounts and a few were
discovered in nature only after having first been synthesized
 Dmitri Mendeleev - Russian chemist who published the first Periodic Table that listed the elements by
increasing atomic mass and arranged so that elements with similar chemical properties would be
in one column.
 The modern Periodic Table places the elements according to the number and arrangement of the
electrons in the atom.
 The elements are arranged according to increasing atomic number.
 The Table is divided into horizontal rows and vertical columns.
 Each box represents an element.
 The vertical columns are called Groups and are labeled with Roman Numerals.
 The horizontal rows are called Periods indicated by Arabic numbers.

The Modern Periodic Table (The Nos. Above the symbols are the Atomic Nos.)

Groups
Group IA – are active metals also called Alkali Metals composed of Hydrogen, Lithium, Sodium,
Potassium, Rubidium, Cesium.
 • All elements of the group except for H+ are metals and have similar properties:
 All of the elements in this group have 1 valence electrons.
 They have similar chemical properties because they have the same number of valence electrons.

Valence Electrons – defined as the electrons located at the outermost energy level (or at the highest
energy level)

Group II A - Alkaline Earth Metals

• They are metals similar to those of I-A but are less active.
• All of the elements in group IIA have 2 electrons in their outermost energy level or 2
valence electrons
• Elements: Beryllium(Be), Calcium(Ca), Strontium(Sr), Barium(Ba), Radium(Ra)

Group III A - Boron Group

o All have 3 valence electrons.

 Elements: Boron(B), Aluminum(Al), Gallium(Ga), Indium(In),Thallium(Tl)

Group IVA – Carbon group
• They have 4 valence electrons.
• Elements are caomposed of metals, metalloids and non-metal
• Elements:Carbon(C), Silicon(Si), Germanium(Ge), Tin(Sn), Lead(Pb),
Group VA – Nitrogen group
• They have 5 valence electrons.
• Elements are caomposed of metals, metalloids and non-metal
• Elements:Nitrogen (N), Phosphorus (P), Arsenic (As), Antimony(Sb) Bismuth (Bi)
Group VIA – Chalcogens (oxygen Family)
• They have 6 valence electrons.
• Elements are caomposed of metals, metalloids and non-metal
• Elements: Oxygen(O), Sulfur(S), Selenium(Se), Telluriom(Te), Polonium(Po),

Group VIIA – Halogens

• They are non-metals and all have 7 valence electrons.
• Elements: Fluorine(F), Chlorine(Cl), Bromine(Br), Iodine(I), Astatine(At)
Group VIII A - Noble Gases
• Also known as Group O elements.
• All except He have 8 valence electrons.
 • Also known as inert gases because they are usually not reactive.
• The 8 electrons in the outermost shell corresponds to filled s and p orbitals which lead to great
stability.
• Elements: Helium (He), Neon(He), Argon(Ar), Krypton(Kr), Xenon(Xe), Radon(Ra),

Generally, the A Group indicates the number of valence electrons an element has. The Group number
of the element is also its valence number.

The B Group elements are called the Transition Metals.

They are all metals and usually have 2 electrons in the outer energy level.
o They are located in the center and at the bottom of the periodic chart.

Periods

 The horizontal rows are called Periods indicated by Arabic numbers.

The maximum number of Periods in the Periodic Table is 7.
The Period corresponds to the Number of Energy Levels an Element has.

Example: Hydrogen and Carbon

The electronic structures of hydrogen and carbon drawn as:

Hydrogen has 1 electron which is on the 1st Energy Level. So it is located at

the 1st Period.

Carbon is located at Period 2 which means that it has 2 Energy levels.

The circles show energy levels - representing increasing distances from the nucleus. You could straighten
the circles out and draw the electronic structure as a simple energy diagram.

Sample Problem: Chlorine has an atomic no of 17.

Using the Periodic Table, a) in what Group is it? _____
b) in what Period is it? _____
c) How many valence electrons does it have? __

Ans: a. VIIA_ b. _3rd Period c. 7

Metals and Non-

Metals

Note the zigzag

line starting from
Boron (B) down
to Polonium (Po).
These are called
metalloids. Those
at the left of the zigzag line are the Metals and those at the right side of the metalloids are the non-
metals.

5. Teaching and Learning Activities

Exercise:
1. Given the data on the Elements complete the Table below:

Element Atomic No. Atomic Mass Protons (P+) (e-s) N

Si 14 14
Fr 223 87
Ir 77 115
At 85 210
O 8 8

II.1. A. An element has an Atomic No. of 16.

a. How many electrons does it have? ____
b. How many protons does it have? _____
c. In what Group is it? _____
d. In what Period is it? _____
e. What is its symbol? _____
f. Is it a metal or a non-metal?
2. A. An element is located in Group VIIA and Period 4
a. How many Energy Levels does it have?
b. How many valence electrons does it have? _____
c. Is it a metal, a non-metal or metalloid? _____
e. What is its symbol? _____
3. Write the electronic configuration of the following elements using the a)subshell notation,b) the noble
gas abbreviated notation and c) orbital diagram
a. Carbon 6
b. Chlorine 17
c. Oxygen 8

III. Discussion. Answer briefly but substantially.

1. How important are the organic compounds in your life?
2. What are the characteristics of carbon that makes it special?

6. Recommended learning materials and resources for supplementary reading.

Modules
 Periodic Table
Exercises
Video Presentation

7. Flexible Teaching Learning Modality (FTLM) adopted

1. Edmodo
2. google classroom
3. module

8. Assessment Task

Name:______________________________ Course & Section _______ Score. _________

I. IDENTIFICATION. Identify what is called for;

_______________________1 The Swedish chemist who expressed the difference between compounds
from living organisms (as organic) and compounds from minerals (as inorganic) organic) and
compounds from minerals (as inorganic).
_______________________2.The scientist who dispelled the vital force theory.
_______________________3. Russian chemist who proposed the first Periodic Table that arranged the
elements according to increasing atomic mass.
_______________________4. Defined as the smallest particle of matter that retains alll the properties of
that matter.
_______________________5. Positively charged particles located inside the nucleus of an atom
_______________________6. Negatively charged particles located inside the nucleus of an atom
_______________________7. Atomic particles having no charge or neutral.
_______________________8. The number that pertains to the Number of Protons
_______________________9. This number is equal to the number of protons plus numbber of neutrons
_______________________10. They are also known as transition elements.
_______________________11. Term used for the electrons located at the outermost or highest energy
level.

_______________________12. The Group A in the Periodic Table represents _____.

_______________________13. It corresponds to the number of Energy levels present in the atom.
_______________________14. The Group which are also known as Halogens.
_______________________15. Defined as the number of electron at the outermost Energy Level.
_______________________16. The term used for elements that are along the zigzag line in the Periodic
Table.
_______________________17. The term used for elements located at the left of the zigzag line in the
Periodic Table.
_______________________18. The term used for elements located at the right of the zigzag line in the
Periodic Table.
_______________________19. Referring to the Periodic Table what element is present at Group IIIA
Period 5.
_______________________20. What element is located at Period 3 Group VIA in the PT.

II. Multiple Choice.

1. An element is on the 4th Period in the Periodic Table. Which of the statements is true? .
a. It has 4 protons b. . It has 4 neutrons
c. It has 4 valence electrons d. 3. It has electrons filled up to the 4th Energy
level.
 2. . An element is located in Group IIA in the Periodic Table. Which of the statements is true? .

a. It has 2 valence electrons

b. It has electrons filled up to the 2nd Energy level.
c. It has 2 protons
d. It has 2 neutrons
3. If an Element has an atomic Mass of 45 and an atomic No. of 22, which of the statements is true? .
a. It has 45 protons b. . It has 23 protons
c. It has 45 electrons d. It has 23 neutrons
4. The element located at the 4th Period Group IIA is
a. non- metal b. metalc. metalloid d. transition element
5. What element is present in Group VA Period 3
a. In b. P c.As d. Ta

III. Answer the questions on the blank.

An element has an Atomic No. of 56.
a. How many electrons does it have? ____
b. How many protons does it have? _____
c. In what Group is it? _____
d. In what Period is it? _____
e. What is its symbol? _____
f. Is it a metal, non-metal or metalloid?
9. References (at least 3 references preferably copyrighted within the last 5 years, alphabetically
arranged)
1. Carey, Francis A.2001. Advanced Organic Chemistry Springer
2. Olmsted ,John and Gregory M. Williams.1996.  Chemistry: The Molecular Science Jones &
Bartlett Publishers. 366-371
3. Wade , L. G., Jr. 2003. Whitman College Organic Chemistry Fifth Edition
4. https://www.sigmaaldrich.com/technical-documents/articles/biology/periodic-table-of-elements-
names.html
ISUE__ __ Syl ___
Revision: 02
Effectivity: August 1, 2020