EM Agravante Module 1 Organic Chem
EM Agravante Module 1 Organic Chem
EM Agravante Module 1 Organic Chem
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Course GEE-C
Course Description Chemistry
Course Overview
This course is designed to introduce Organic Chemistry to college students. It is divided into five
units or major sets of topics. They are:
UNIT 1 Historical Background of Organic Chemistry;
UNIT 2 Hydrocarbons and Organic Structures, Bonding and Hybridization;
UNIT 3 Classification of Organic Compounds, Derivatives of hydrocarbons, IUPAC and
Common names, Structures, Properties and Uses;
UNIT 4 Introduction to Reactions of Organic Compounds; and
UNIT 5 Common Reactions involving Aliphatic Hydrocarbons.
This Module entitled Introduction to Organic Chemistry as study material is the first of the
three-part set, written and prepared to help the students in their study of the field. Module 2 and
Module 3 follow this Module 1 to complete the series for the study of the subject. As a
stand-alone learning material, this guides and assists the students in their learning activities to be
able to achieve the desired learning objectives and outcomes for the course in organic chemistry.
This module has been prepared following the Outcomes-based syllabus which contain the
important concepts for the study of organic chemistry. It is in the sequence to help the students in
gaining understanding of the concepts and building of competencies required by the discipline of
organic chemistry. However, the students can access this module randomly from any part or page
depending on his/her study requirement. The author sees this material is best helpful to students
when complemented with other reference materials (from the internet or other sources) for them
to validate the understanding.
It is the hope of the author/instructor of the subject that the students enrolled in this course will
find the subject fascinating; that they will be able to generate and gain the very crucial knowledge
and understanding of the concepts in organic chemistry and a lot of the organic substances
around. The competencies that they can develop can help them on their awareness and
self-growth. The students can also refine their common sense, and improve to reassess their
choices. Most importantly, the knowledge and understanding of the concepts in organic chemistry
can help the students develop their ability to predict, just like in predicting the products in the
reactions, therefore, can help them invest in good and avoid not good situations. Therefore, the
students can be prepared to take charge of his lifelong learning.
1.1 Atomic structure of carbon and other elements commonly found in organic compounds;
• accounting of electrons and lewis structures of organic molecules including isomeric and
resonance structures;
• general formula, molecular formula, empirical formula, skeletal formula;
1.2 Bonding in organic compounds
• hybridization and geometry
• Intermolecular and intramolecular forces of attraction
• Lewis and Bronsted-Lowry acids and bases
1.3 General properties of organic compounds
• electrical conductivity, flammability, rates of reaction, abundance, etc.
• natural and synthetic
Organic Chemistry
The study of the structure, properties, composition, reactions and preparation of
carbon-containing compounds, which include not only hydrocarbons but also compounds with
any number of other elements, including hydrogen (most compounds contain at least one
carbon-hydrogen bond), nitrogen, oxygen, halogens, phosphorus, silicon, and sulfur.
This branch of chemistry was originally limited to compounds produced by living organisms but
has been broadened to include human-made substances such as plastics. The range of application
of organic compounds is enormous and also includes, but is not limited to, pharmaceuticals,
petrochemicals, food, explosives, paints, and cosmetics.
Organic compounds are all around us. They are central to the economic growth of the many
countries. Rubber, plastics, fuel, pharmaceuticals, cosmetics, detergents. Coatings, dyestuff, and
agricultural industries, to name a few. The very foundations of biochemistry, biotechnology, and
medicine are built on organic compounds and their role in life processes. Many modern, high-tech
materials are at least partially composed of organic compounds.
Organic Compounds. An organic compound is defined as any compound whose molecules contain
carbon and hydrogen (also known as ” hydrocarbons”) or compound that is the derivative of it.
The branch of science which deals with the scientific study of structure, properties and reactions
of hydrocarbons and their derivatives is known as organic chemistry.
The study of Organic Chemistry make us review some ideas about atoms, bonds, and molecular
geometry that you may recall from your general chemistry course. Some concepts in this chapter
are likely to be familiar to you, and it’s important to make sure you understand them before move
to the concepts in the study about organic compounds.
1. Explore your home and list five (5) organic compounds that are naturally
produced.
2. List five (5) synthetically produced items which are organic compounds (or may
contain at least one) that are sold in the supermarkets/grocery stores.
The atomic structure of carbon atom is illustrated in Figure 1 above. From the atomic number of
carbon of 6, it is shown that there are 6 protons and 6 neutrons at the core, which is the nucleus.
Outside, the 6 electrons revolve following the orbits around the nucleus. Further, the protons
carry the 6 positive charges, while the neutrons carry no charges, hence neutral, and the electrons
carry the negative charges. Furthermore, a neutral atom contain equal positive and negative
charges.
Hereunder, in Figure 2 which shows the atomic structure of hydrogen (left) and oxygen (right). The
nucleus for hydrogen is shown as the black core, while that of oxygen is in gray. The subatomic
particles and the electrons on the outermost energy levels or shells of each are also shown. These
electrons on the outermost energy levels are referred to as the valence electrons.
How are the electrons distributed in an atom? In the quantum mechanical model of atomic
structure, the behavior of a specific electron in an atom can be described by a mathematical
expression called a wave equation—the same sort of expression used to describe the motion of
waves in a fluid. The solution to a wave equation is a wave function, or orbital, denoted by the
Greek letter psi, Ψ. An orbital can be thought of as defining a region of space around the nucleus
where the electron can most likely be found. What do orbitals look like? The figure below , Figure
3 depicts the s and p orbitals.
There are four different kinds of orbitals, denoted s, p, d, and f, each with a different shape. Of the
four, we’ll be concerned only with s and p orbitals for now because these are the most common in
organic and biological chemistry.
Figure 4. The Energy Levels of electrons in the atom. The orbitals are filled to maximum capacity.
EM AGRAVANTE ORGANIC CHEMISTRY MODULE 13
In the similar fashion above, the ground-state electronic configuration of the elements hydrogen,
carbon and phosphorus are shown in the Figure 5 below.
The occupied orbitals of the three energy levels of the atomic structure of these elements are
shown. Take note of the partially filled orbitals of the outermost energy levels of each. The
electrons on the outermost energy levels are referred to as the valence electrons.
Now that you have gained the understanding of the concept on the atomic structure of the
elements and the arrangement of the subatomic particles both inside and outside the nucleus,
you will find it easy to work on the electronic configuration, and onward to the determining of the
valence electrons of the elements in the periodic table. Be familiar with the mnemonic pattern
and be able to relate it to the concepts that you need to learn as you progress in your study of the
subject on organic chemistry.
At this point, you are now ready for the next exercise.
EXERCISE NO. 1
Electronic Configuration and Valence Electrons
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Instruction: Answer the following questions showing detailed account on the space below on
how you arrive at your answer.
Upon the start of the study of this Unit 2, it is imperative for the learner to have a review of some
ideas learned from general chemistry for an easier understanding of organic chemistry.
The completion of this unit requires that you will be able to:
Hybridization of Carbon
With the tetravalent carbon atoms, the situation in organic compounds is complicated as
compared to the bonding that hydrogen makes in the H2 molecule. As observed in the methane
molecule, carbon has four valence electrons (2s2 and 2p2). The s and p orbitals combine or
hybridize, to form four equivalent atomic orbitals with tetrahedral orientation.
Source:file:///C:/Users/acer/Documents/McMurry%20J.E.%20-%20Fundamenta
ls%20of%20Organic%20Chemistry,%207th%20ed.%20-%202010.pdf
Here is another approach of how the hybridization of carbon is illustrated. Notice how the
movement of the electrons are shown from the ground state to the individual excited states upon
hybridization.
The concept of hybridization explains how carbon forms four equivalent tetrahedral bonds but not
why it does so. The shape of the hybrid orbital suggests the answer. When an s orbital hybridizes
with three p orbitals, the resultant sp3 hybrid orbitals are unsymmetrical about the nucleus. One
of the two lobes is much larger than the other and can therefore overlap better with another
orbital when it forms a bond. As a result, sp3 hybrid orbitals form stronger bonds than do
unhybridized s or p orbitals.
A simple way of indicating the covalent bonds in molecules is to use what are called Lewis
structures, shown in Figure 9, or electron-dot structures, in which the valence shell electrons of an
atom are represented as dots. Thus, hydrogen has one dot representing its 1s electron, carbon has
four dots (2s2 2p2), oxygen has six dots (2s2 2p4), and so on. A stable molecule results whenever a
noble-gas configuration is achieved for all the atoms—eight dots (an octet) for main-group atoms
or two dots for hydrogen. Simpler still is the use of Kekulé structures, or line-bond structures, in
EM AGRAVANTE ORGANIC CHEMISTRY MODULE 17
which a two-electron covalent bond is indicated as a line drawn between atoms.
Figure 9. The methane molecule in Lewis Structure; four sp3 hybrid orbitals;
sigma bonds of methane;
When two sp2-hybridized carbon atoms approach each other, they form a strong bond by
sp2-sp2 head-on overlap. At the same time, the unhybridized p orbitals interact by sideways
overlap to form a second bond. Head-on overlap gives what is called a sigma (δ) bond, while
sideways overlap gives a pi (π) bond. The combination of sp2–sp2 overlap and 2p-2p π overlap
results in the net sharing of two electron pairs and the formation of a carbon–carbon double
bond . Note that the electrons in a bond occupy the region centered between nuclei, while the
electrons in a pi (π) bond occupy regions on either side of a line drawn between nuclei.
The results of the experiments show that the four C-H bonds in the simplest organic molecule, CH4
(methane) are equivalent. Meaning the orbitals used for bonding are the same. This is not
consistent with the excited configuration of carbon showing one different orbital 2s and three
equivalent orbitals 2p.
• Further explanation: Four atomic orbitals from the “excited” carbon undergo hybridization
to form equivalent orbitals. The s orbital and all three p orbitals have been mixed, thus
forming sp3 hybrid orbitals. Why sp3?
The four sp3 hybrid orbitals will arrange themselves in three-dimensional space to get as far apart
as possible (to minimize repulsion). The geometry that achieves this is tetrahedral geometry,
where any bond angle is 109.5o . Now, we can picture out a 3-dimensional structure of methane
as shown below. ( Recall VSEPR theory)
Compare the structure of methane to that of ethane below, where the bonds formed are also
sigma bonds. The structure of ethane shows the formation of the sigma bonds which result from
the head-on overlap of the sp3 orbitals of 2 carbon atoms, and sigma bods formed from sp3
orbitals of carbon and the 1s orbitals of hydrogen.
EXERCISE NO. 2
Hybridization and Molecular Geometry
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Ethane. Now it’s time look at ethane. Just like methane, it also uses the four sp3 orbitals. Three of
these sp3 orbitals of one carbon are bonded to hydrogens, one is bonded with the other carbon
atom. All bonds formed are sigma bonds. This is illustrated in Figure 11 below.
Ethene. Now it’s time look at ethene or ethylene. The three atoms are attached to each carbon
atom, showing a double-bonded carbon atom. Instead of forming four hybrid orbitals like
methane, ethene only requires three hybrid orbitals. The s orbital and two of the p orbitals for
each carbon have been mixed forming three sp2 hybrid orbitals, leaving one pure (unhybridized) p
orbital to form a double bond.
The three sp2 hybrid orbitals will arrange themselves in three-dimensional space to get as far
apart as possible. The geometry that achieves this is trigonal planar geometry, where the bond
angle between the hybrid orbitals is 120o . The unmixed pure p orbital will be perpendicular to
this plane.
The more elaborate projection of the covalent bonds of the compound ethene is shown in Figure
13 below. The two sp2 orbitals form a sigma bod in the head-on overlap fashion.
Another depiction of the formation of sigma bonds and the pi bond in the molecule ethene is
presented in Figure 14. The sigma bond results from the head-to-head overlap of the two sp2
orbitals of the two carbon atoms. The pi bond results from the side-to-side overlap of the pure
unhybridized p orbitals of the two carbon atoms. In the formation of the carbon-to-carbon double
bond, one is sigma bond, another is the pi bond.
1. What is the hybridization of carbon for acetylene? The Lewis structure is given below.
We have two tables here which present guides to the types of organic compound formulas.It is
important for one studying organic chemistry to be familiar to each of these formulas and be able
to distinguish one from the others.
The Structural Theory of Organic Chemistry. Constitutional Isomers: Different compounds that
EM AGRAVANTE ORGANIC CHEMISTRY MODULE131
have the same molecular formula but differ in the sequence in which their atoms are bonded,
that is, their connectivity but not number of bonds (older term: structural isomers).
Methylpropane and butane molecules as projected above, in Figure 14, have the same molecular
formula of C4H10, but are structurally different (methylpropane on the left, butane on the right).
The molecular formula of methylpropane or isobutane is also C4H10, (derived from the structural
formula by counting the number of carbon and hydrogen). However, chemists often use
condensed structural or line angle formulas because structural formulas take a lot of space.
C5H12
Instruction:
Structures of more complex organic compounds are drawn using a combination of line angle and
condensed structural types, as shown for compound A and B below.
Instruction:
Convert the following skeletal structures into molecular formulas, and tell how many hydrogens are
bonded to each carbon:
EXERCISE NO. 9
Structural Formulas
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Instruction:
Instruction:
The following molecular model is a representation of para-aminobenzoic acid (PABA), the active
ingredient in many sunscreens. Indicate the positions of the multiple bonds, and draw a skeletal
structure (gray C, red O, blue N, ivory H).
In the earlier lessons, you learned about the general concepts of on organic chemistry and
chemical bonding, the different types of formulas, and some basic behavior of representative
organic compounds. Now it’s time to look at the classification of organic compounds. This unit will
introduce you to the most common classes of organic compounds.
What will you learn? This unit will introduce the most common classes of organic compounds.
Upon completion of this unit, you will be able to:
EXERCISE NO. 11
Organic Materials
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Instruction:
Classify each given samples whether organic or inorganic. For your remarks, write a phrase or
a statement as basis for your answer.
Now that you have ably identified materials already to be organic or inorganic, you are now ready
to examine the basic differences between organic and inorganic compounds in terms of their
characteristics. The understanding of their differences prepares the learner for the study of
organic chemistry, the organic compounds and their properties and behaviors. On the table below,
a comparison of distinct characteristics of these two groups of compounds.
While inorganic compounds are classified into acids, bases, oxides, and salt, organic compounds
are classified according to families. The presence of a functional group determines the family or
class of an organic molecule. A functional group is a part of an organic molecule responsible for its
physical and chemical reactivity. Why is it important to recognize functional groups of organic
compounds? Functional groups allow correct classification. It can be used to make a reasonable
prediction on how a compound will behave or react given certain conditions.
Knowing the properties and reactivity of organic materials is important to maximize its use and
proper handling. Especially in dealing with toxic organic compounds and those known as
carcinogens.
The tables below presents Structures of Some Common Functional Groups. For each class or
family of organic compounds are given the functional group, the general formula, and the name
ending. On one table below, examples are also provided.
For your effective familiarization of the classification of organic compounds, here is a checklist of
important things to remember:
For simple molecules, it is easy to identify classification. For complex molecules, it is important to
analyze the given line-angle structure to determine the functional group.
Understanding chemical structures and functional groups is a crucial part of drug development.
After months of dealing with this pandemic brought about by COVID-19, researchers are still
trying to look for possible treatment. Currently, no medication is recommended to treat COVID-19,
and no cure is available. At present, the aim is just to relieve symptoms by taking pain relievers,
ibuprofen, or acetaminophen ( see structures below). Test III. Part A. Locate and label functional
groups of paracetamol and ibuprofen