INTRODUCING

ORGANIC CHEMISTRY!
Created by Gab Paragas for
University of Santo Tomas
SCHOLIA TUTORIAL CLUB
(Monthlies 2012)

NOTE TO REVIEWEES:
This PowerPoint presentation is an intellectual property of
Ramoncito Gabriel O. Paragas of UST Pharmacy. This was
created to aid in the review of fellow Pharmacy, Med Tech,
and Biochem students taking the course. This presentation is
not definitely complete, and is not a substitute to self-study
and note taking. This is created for Scholia Tutorial Club.
Any unauthorized and improper use of this presentation is
prohibited.

WHAT IS CARBON?

Carbon is the head of the Carbon Family

(IV-A) in the periodic table. Carbon is the
basic component of ALL ORGANIC
COMPOUNDS. What then makes Carbon so
special that it is the subject of interest of this
course?

WHAT IS CARBON?

Carbon is always on excited state.

Having basic knowledge of its location in the

periodic table, lets take a look on its
electronic configuration to assess this
property.

WHAT IS CARBON?

Carbon is always on excited state,

making it want the maximum reactions.

Carbon as a part of IV-A Family has four

valence (outer) electrons; it can share all
the valence electrons, forming four strong
COVALENT BONDS.

WHAT IS CARBON?

Carbon atoms can bond with one

another, forming long chains and even
rings.

Of all other elements, carbon alone has

the ability to form an immense diversity
of compounds.

WHY STUDY ABOUT CARBON?

Studying the properties of carbon and the

different reactions it can have with other
elements is important. Why? Simple. Carbon had
been an unexplainable vital force that puzzled
many scientists centuries and decades ago.

WHY STUDY ABOUT CARBON?

Carbon has been the basic component of all the
organic compounds that build you. Your cells are
made up of some carbon-containing compounds.
Reactions in your body cannot proceed without
interference of carbon-containing compounds. The
food you eat; the meat, the vegetables, the fruits they are made of carbon-containing products. The
aroma of coffee, or the taste of fresh apples are all
sensed because of some carbon-containing
products. Even organic compounds cause you to cry,
fear, laugh and fight.
Why study Organic Chemistry?
Simple. Because, youll need it to pass your course.

WHAT DO WE EXPECT FROM

ORGANIC CHEMISTRY?
More Carbon-containing compounds, their nomenclature
and reactions.
Review on some basic chemical principles, and some new
applications in this chemistry.

Application of principles related to your course: In fact,

Org Chem is a Major Prerequisite to many other courses.
Pharmacy:

organic reactions in relation with

pharmacokinetics, pharmacodynamics, and pharmaceutical
chemistry
Medical Technology: determination of presence of organic
compounds in blood and body substances
Biochemistry: the biological application of organic reactions
concerning natural biomedical functions

POINTERS FOR
ORGANIC CHEMISTRY LECTURE MONTHLIES
Introduction to Organic Chemistry:
Understanding the Nature of Organic
Compounds
Structure and Bonding: Acids and Bases

Polarity
Acidity

and Alkalinity

Functional Groups
Structural Effects
Isomerism, and Basic Interpretations of
Structures

MIND MAP
Organic
IntroChemistry
Acid-Base
to CarbonMonthlies
Chemistry

INTRODUCTION TO ORGANIC
CHEMISTRY:
UNDERSTANDING THE NATURE
OF ORGANIC COMPOUNDS

INTRODUCTION TO ORGANIC CHEMISTRY:

UNDERSTANDING THE NATURE OF ORGANIC
COMPOUNDS
First things first. Let us all ask ourselves, WHAT IS
ORGANIC CHEMISTRY and WHAT DOES IT
STUDY?
Organic Chemistry is the chemistry of carboncontaining compounds. It studies the nature of carbon,
the nature of its compounds, the nature of its reactions.
It touches your life, taking you through a fascinating
undertaking.
From studying small basic blocks of your life,
understanding organic chemistry will influence the way
you think about larger, more complex things. Example of
organic assemblies are cells, viruses, bacteria and guess
who? OURSELVES.

ORGANIC CHEMISTRY VS
INORGANIC CHEMISTRY
Organic Chemistry

Inorganic Chemistry

Studies Carbon compounds.

Compounds studied mostly come from living

sources.

Compounds can decompose naturally.

Studies any compound.

Compounds studied are mostly

derived from minerals.
Compounds are decomposable by
energy.

WHAT ARE ORGANIC COMPOUNDS?

Carbon-containing compounds
Naturally occurring; mostly of life origin, and
nature based.

However,

not all organic compounds are not derived

from living organisms, of course. Newly discovered
organic compounds were merely synthesized even
derived from non-organic compounds, or products of
laboratory tests.

Exceptions: CO2, H2CO3, CO3-, CN-

NATURE OF ORGANIC MOLECULES

Of all the hundred plus elements in the
periodic table, Organic Chemistry is mostly
concerned only for ten! Okay, so Carbon is given.
The other nine are:
Hydrogen:
H
Carbon Group: C, Si
Nitrogen Group:
N, P
Oxygen Group: O, S
Halogen Group: F, Cl, Br, I

NATURE OF ORGANIC MOLECULES

There are about 37 million known organic
molecules.
There are rules that nature follow that help us
understand that organic molecules rest largely on
understanding of small combinations of atoms.
So instead of 37 million separate compounds that
we study for some random reactivity, there are
only about a dozen families of chemistry whose
chemistry is predictable.

FUNCTIONAL GROUPS

A group of atoms within a larger molecule that

has a characteristic chemical behavior.
Simpler: a certain group, or part of a molecule
that has specific function. That function is to
react, and behave in a certain manner the
time an attack of another molecule comes.

FUNCTIONAL GROUPS:
C-C MULTIPLE BONDS
Alkanes: most basic bonding of carbon to
another carbon. Single bonds (sigma bonds/ )
connect these carbons, and mostly hydrogen
atoms take the place of empty spaces. H3C-CH3
Alkenes: double bond between carbons (one
sigma, one pi bond/ ). H2C=CH2
Alkynes: triple bond between carbons (one
sigma, two pi). HC=CH

GREEK PREFIXES IN NAMING

COMPOUNDS
Number of

Prefix

Example

Meth-

Methane

Eth-

Ethene

Prop-

Propene

But-

Butene

Pent-

Pentane

Hex-

Hexyne

Hept-

Heptyne

Oct-

Octane

Non-

Nonane

10

Dec-

Decane

Carbons

CHARACTERISTICS OF COVALENT
BONDS
Bond

Bond

Bond

Bond Angle

Hybridization

Strength

Length

CC

340 kJ/mol

154 pm

109.5

sp-sp

C=C

610 kJ/mol

133 pm

120

sp-sp

C=C
830 kJ/mol
120 pm
180
sp-sp
Covalent bonds are bonds exhibiting equal sharing of electrons
between atoms. These bonds are stable, and they have limitations
to attractions.

Condition: Atoms cannot stay close together (repulsion) and

cannot go to far from one another (loss of attraction). Just the
right distance.

What can you infer from the table above?

CHARACTERISTICS OF COVALENT
BONDS

Given that Carbon is

tetravalent, and
always at excited
state, take a look at
the equal sharing of
electrons in Methane;
the most fundamental
and saturated organic
compound.

DEFINING
BOND LENGTH AND BOND
STRENGTH
Bond

Bond

Bond

Bond Angle

Hybridization

Strength

Length

CC

340 kJ/mol

154 pm

109.5

sp-sp

C=C

610 kJ/mol

133 pm

120

sp-sp

C=C

830 kJ/mol

120 pm

180

sp-sp

Bond strength is the energy requirement to

form a bond between two atoms. It is also the
energy requirement necessary to break the bond
between atoms.
Bond length is the optimum distance between
that enables two atoms to attract each other. Not
too close, and not to far.

THE PRINCIPLE OF BOND ANGLE

Bond

Bond

Bond

Bond Angle

Hybridization

Strength

Length

CC

340 kJ/mol

154 pm

109.5

sp-sp

C=C

610 kJ/mol

133 pm

120

sp-sp

C=C

830 kJ/mol

120 pm

180

sp-sp

Remember the person that irritates you? Carbon

also wants to maintain a distance to other
carbons. They get irritated if they stay too close
than tolerable for each other. Thus, when a chain
is formed, a slight bending of bonds occur.
Bond angle is the measure of bending that
occurs shall bonding be present. The more bonds,
the straighter the chain (see the C=C bond).

HYBRIDIZATION
sp3-sp3: single bond
between atoms. The sp3
orbital is shaped long
enough, giving you a long
sigma bond.
sp2-sp2: double bond
between atoms.
sp-sp: triple bonds
between atoms
All these hybridization
statuses are depending
on the number of
valence/ outer electrons.

HYBRIDIZATION: CHARACTER

sp3
sp2
sp
s

character

Character

px

py

pz

25%

25%

25%

25%

33%

33%

33%

-------

50%

50%

-------

-------

100%

-------

-------

-------

Always treat the bond as a 100% character

then divide. Question: Which hybrid has the
least s character?, the greatest y character?

HYBRIDIZATION

Direction: Identify the hybridization of the

carbons present in the molecular structure of 2,2dimethylbut-2-ene.
Draw the structure:

Tip: To assess, always prioritize the stronger

bond (double/ triple).

FUNCTIONAL GROUPS:
CYCLICS AND AROMATICS

Given again, Carbons can form long chains, it can

also branch and join together, forming chains or
rings. Hydrogen atoms take the place of remaining spots
of the tetrahedron. These are called cyclics.
Notice the conformation of cyclohexane. In the past, it
has been a big mystery on what differentiates organic
compounds with odor and without. August Kekule
noticed in his experiments that there is such a compound
having six carbons matching with 6 hydrogen
atoms, forming a ring with three double bonds;
exhibiting odor, but doesnt have the characters of
alkenes. This was later called benzene. This is the base
functional group of aromatic compounds.

FUNCTIONAL GROUPS:
CYCLICS AND AROMATICS
Cycloalkane

Benzene/ Aromatic

C6H12

Has the same formula as a typical hexene.

Has no smell.

C6H6

Has the unusual case of equal

number of carbon and Hydrogen.

Has odor/ fragrance.

FUNCTIONAL GROUPS:
CARBON SINGLY BONDED TO AN
ELECTRONEGATIVE ATOM
Name

Structure

Name

Example

Ending
Alkyl

Bond

R-X

---------------

CH3Br

Alcohol

R-OH

-ol

CH3CH2OH

Ether

R-O-R

ether

CH3OCH3

Halide

(alkoxy

Carbon

alkane)
Amine

R-NH2

-amine

CH3NH2

Thiol

R-SH

-thiol

CH3SH

Sulfide

R-S-R

sulfide

CH3SCH3

FUNCTIONAL GROUPS:
CARBONYL GROUPS

These are functional groups with a C=O group, called the

carbonyl group (car-bo-neel).

Priority groups: In decreasing Priority

Carboxylic
Acid

acid

Anhydrides

Esters
Thioesters
Acid

halides

Amides
Nitriles
Aldehydes
Ketones

STRUCTURE AND BONDING:

ACIDS AND BASES

POLARITY OF ORGANIC
COMPOUNDS

Polarity results from unequal electronegativities

of elements.

If the electronegativity difference is is 0.0 to 0.49

only, it is non-polar.
0.5- 1.99; Polar.
2 and above; Ionic.

Non-polarity occurs at moment where pull to a

direction is neutralized by an opposing pull.

POLARITY OF ORGANIC
COMPOUNDS
Heres the thing you always have to remember
about polarity: if there is inequality of
electronegativity (ability to attract other atoms to
itself), there is taking poles; a partially positive
(+) pole and a partially negative (-) pole,
thus the name polar. (Also called dipole.)

Remember that the direction of attraction is always

headed to the partially negative side. (The
negative side has the bigger electronegativity
value). Carbon is most likely the positive pole. The
arrow looks like
having the tail with
positive pointing to the negative pole.

ELECTRONEGATIVITY

This is the measure of the ability of an atom

to attract other atoms to itself.
It is very important in determining the polarity of
an organic compound. Electronegativity tells
you if a bond is non-polar covalent, polar/
dipole, or ionic.
REMEMBER THIS; this is very useful.
(F>O>N>Br>I>C>H)
In decreasing electronegativity, always
remember Fonbrich.

POLARITY OF ORGANIC
COMPOUNDS
+

C-N
(2.5 3.0)
Notice Nitrogens pull to Carbon. The bigger the
electronegativity value, the more negative,
thus, more attracting/ pull.
As the element is more in the right and upper
side of the Periodic Table, the more
electronegative.

POLARITY OF ORGANIC
COMPOUNDS
Take a look at this example:
+
Li - C
(1.0 2.5)

Is Carbon still positive?

Should a case be that Carbon bonds with a greatly
lesser element in terms of electronegativity, it
becomes partially negative and it aims to pull the
other.

POLARITY OF ORGANIC
COMPOUNDS

What about this example?

CH
(2.5 2.1)
It is unequal, but is it polar?
If you remember, there is a determinant of
polarity called the electronegativity difference.
2.5 2.1 = 0.4
0.4 = NON - POLAR

POLARITY OF ORGANIC
COMPOUNDS

Take a look:

C Cl
(2.5 3.0)
Polar right? But what if there are four Chlorine
atoms that will bond with Carbon, will it still
be polar?
Cl
Cl C Cl
Cl
Poles are neutralized by opposing pulls. N-Polar.

FOR YOUR INFORMATION:

TO MAKE IT SIMPLE
Polar bonding is called a dipole bond.
+

X
:Y
Non-Polar bonding is called an induced dipole;
because it is not polar, inducing the dipolarity of the
bond. Non Polar bonds are also covalent.
Covalent bonds share e- equally between atoms.
X: Y
Ionic bonding is the total giving up of electrons
from a cation, and an anion takes the valence. This
makes a total positive and total negative character, not
partial (polar).
X+ :Y

SOME REVIEW QUESTIONS:

What are acids and bases?

What is an acid according to the BronstedLowry Definition? A base?

What is an acid according to the Lewis

Definition? A base?

ACIDS AND BASES ACCORDING TO

Bronsted - Lowry

Lewis

An Acid is a H+ donor (Proton donation).

A Base is a specie capable of

donating an electron pair or more.

A Base is a H+ acceptor.

Products are called conjugates.

An Acid is an electron pair

acceptor.

Electrons move from the base to

the acid to form products.

RELATIONSHIP OF ACIDITY WITH

STRENGTH OF ORGANIC ACID
Higher Ka
= the stronger the acid
= the higher the acidity
= the lower the pKa
= the lower the pH
Ka is the ionization constant of a weak base; it is
the extent to which an acid shall ionize, and react.
Taking the negative logarithm of Ka (pKa),
takes the pH. The lower the pH, the stronger
the acid or more acidic.

ORGANIC ACIDS
Organic Acids are mostly compounds having the
Carboxylic Acid Group or the C=OOH group.
The longer the chain, the less acidic.

If there is an unusual atom, like a electrophile/ electronrich atom (F, O, N, Cl, Br, I), it is acidic. Take note that
the halogen atoms (except F) are components of strong
acids. They make the compound acidic. The nearer they
are to the C=OOH, the more acidic.
Branching decreases the acidity. Why? Because
branching creates bulkiness, thus the steric effect. If there
is steric effect, the more atoms will be fighting for the
lone electrons of the carboxyl group. Thus less acidic,
more basic.

ORGANIC BASES
Organic Bases are mostly composed of a chain
..
with an amine NH2, the basic component of the organic base.
There is a lone pair above the amine, and the more available it
is, the more basic.
The longer the chain attached to the amine, the less available
the lone pair for bonding.

Branching as well decreases the alkalinity of an organic base.

Steric effect as well decreases the alkalinity, because bulkiness
twists the molecule, making more atoms fight for the lone pair for
bonding.
Take time to see that if an electron rich atom/ component of a
strong acid is attached to the organic base, it becomes less and
less acidic, because it gets neutralized.
The nearer the electrophile to the amine, the less basic the
compound as a whole.

FORMAL CHARGE:

Lewis dot structure is very important when it

comes to solving the formal charge. Formal
Charge is the excessive charge present in a
compound because of pull of electron rich
elements.
Formal Charge =
Valence e Bonded e unshared electrons

Simpler Formula of Formal Charge =

Valence e Bonds around the atom unshared
e

STRUCTURAL EFFECTS

STRUCTURAL EFFECTS

Structural effects as the name suggests, are

the effects that are evident or occurs because
of the structure of an organic compound.
Occurrence of these effects are very much
considered natural phenomena of organic
chemistry.
We will only discuss seven basic structural
effects, applying stock knowledge from inorganic
chemistry, and what weve just discussed in the
first part of this tutorial.

RESONANCE
(-ELECTRON

DELOCALIZATION)

Lets make it simple: This is an effect mostly

evident with benzene.

It should have at least four sp2 carbons wherein

the -bonds

must be adjacent to each other.

This effect makes benzene stable, because should
an electrophile/ electronegative atom attach to the
ring, the double bonds will go around the ring,
thus, resonance (different structure, same ring).

RESONANCE
(-ELECTRON

DELOCALIZATION)

Why pi electron delocalization? Because only

pi bonds can move; sigma bonds are internally
shielded and strong. Pi bonds move to provide
carbon the necessary tetrahedral bonds.

C-H HYPERCONJUGATION
( - ELECTRON DELOCALIZATION)

Take note, electron, not bond.

Resonance is stronger than this, and has
greater stabilizing effect.
Applicable only to sharing of sigma
electrons between Carbon and Hydrogen,
wherein the C-H bond must be ADJACENT
(directly connected) to an sp2 carbon.

INDUCTIVE EFFECT

This is simply the shifting of electrons in a

sigma bond in response to the
electronegative atom. This is an effect of
attraction, thus, the more electronegative atom
takes the pull to itself, inducing the nearby atom.
This relates to the acidity and alkalinity of
organic compounds
Electron

Carboxylic Acid (R COOH)

Electron

Attracting: acidic

Repelling: alkaline

Amines (R NH2)

STERIC EFFECT

Basically, it is congestion or bulking of

branched substituents, thus making the
whole molecule less reactive.
Cl Cl
C ..
H3C NH2
In the above example, you may notice that there
are some substituents near the amine group.
Because of the congestion, more of these
substituents block the ability of the N lone
pairs to bond.

LONE PAIR DELOCALIZATION

The making of a compound.

Without delocalization, no electron can be
shared within atoms of different elements.

VAN DER WAALS FORCES

(FON-DER-VHAALS)

Forces of interaction between compounds.

It is not ionic.

It is not H-Bonding.

There are three types of these forces.

Dipole-Dipole

Dipole-Induced

Dipole
Induced Dipole-Induced Dipole

VAN DER WAALS FORCES

(FON-DER-VHAALS)
Okay, lets make it sweet and simple.

Dipole means polar, if you remember. Induced

dipole is non-polar covalent, or at least it tries
hard to be polar.
Dipole-Dipole means polar to polar. So you
react two polar molecules, and the force that will
let them interact is called a Dipole-Dipole Force.
CH3-Li
+ CH3OH
Polar - Polar

VAN DER WAALS FORCES

(FON-DER-VHAALS)

Dipole Induced Dipole; Polar to Non-polar.

The force that holds them to interact is called by
the same name.
H3CC=OCH3 CCl4

Polar

Non-Polar

Induced Dipole-Induced Dipole; Non-polar to

non polar. Maybe you get it already?
CCl4 Br-Br
Non-Polar Non-Polar

H-BONDING

An effect of hydrogen atom bonding with a more

electronegative atom.
Take note that H has 1 proton, and 1 electron. If
and only if the one electron of hydrogen is given
up for bonding, then the only one proton remain,
thus H will have a positive charge. This is why it
is sometimes called a proton donation.
Examples:
H Br Hydrogen - bromine
HO
Hydroxide

ISOMERISM, AND
BASIC INTERPRETATIONS
OF STRUCTURES

ISOMERS:
COMPOUNDS WHICH ARE NOT
IDENTICAL BUT HAVE THE
SAME CHEMICAL FORMULA.

Isomers

Constitutional

CONSTITUTIONAL ISOMER
STRUCTURES

Constitutional Isomers are isomers with

relationship to a functional group. This
functional group plays a big role on giving the
compound an identity.
Skeletal: Atom-stick model.
Branched:

when substituents attach to the main

chain.
Straight: you form a straight chain.
Tip:

In the exam, if you are asked to give the

isomer of a straight chain, give a branched
structure; vise-versa. Same goes with the next.

CONSTITUTIONAL ISOMER
STRUCTURES

Positional Isomer: the position of the R

Group, or the functional group is differed.
CH3CH2COOH = CH3COOCH3

Functional Group: give a derivative.

Alkenes

Cycloalkanes
Alcohol Ether
(Alco-Et)
Aldehyde Ketone
(Alco-Ket)
Alkynes Cycloalkenes Alkadienes
Carboxylic Acid Ester
(Carbo-ster)

CONFORMERS

Conformers are a result in the twist of one component

of an organic compound. There are two types of
structures.
Sawhorse: Slant and line bonded. Take note of steric
effect, prevent nearing of two identical elements to form
bulk. Instability occurs when there is steric effect. The
Right conformer is more stable.
Cl Cl
C
Cl C H
H C H C
H H H Cl H
H

CONFORMERS

Newman: a structure where the front and back

of the compound is emphasized.
There are two types of Newman Projection.
Eclipsed and Staggered (Stable).

STEREOISOMERS

Same connection, different representation in 3D.

Geometric: the similarity of sides of two identical/
unidentical substituents.
Cis:

same side
Trans: opposite sides

The rule is that you cut the middle of double bond, then you see if
the compound has the substituents are on the same side or not (ex:
UP - UP). Prioritize the one with a larger atom. no.

STEREOISOMERS

E-Z Rule/ Convention/ Notation: used when

there is a long chain and more than three or
more substituents surrounding the carbons
of a double bond.
Entgegen:

(ent-gay-guhn) opposite sides.

Prioritize the one with a higher atomic number.
(German for Opposite)

Zusammen:

(tsu-zah-mhn) same side. Still

prioritize the atoms with higher atomic number.
(German for Together)

SOME POINTERS AND

ADVICE

GENERAL:
In Organic Chemistry Course, Lecture only has a
monthly exam.
The monthlies of the Lecture is equivalent to 20% of the
total Org Chem grade.

Lecture long exams for monthlies are usually a 100%

to a hundred items, meaning if you already made two
mistakes, you have a grade of 98%. Ratio is 1:1.
Passing grade is 75%, however this is still adjustable,
like the quizzes. Aim for Gold!
For those wondering, nomenclature is not a part of the Lec
Monthlies, but basic knowledge of this is an advantage.

TIPS AND ADVICE

Before the exam, obtain all necessary reviewers and
prepare yourself.
Do not cram.
About 12 to 24 hours before the exam, do not review and
try to relax. Just make quick browsing on your notes. This
prevents you from forgetting some of the most important
principles.
It is useful to memorize values.
Make sure you have your permit (if issued), and your
writing aids. If calculators and other tables are allowed,
bring them. Prepare them the night before.
On the exam day, be at the venue about 30 minutes before
the exam. This will relax you, and give you time for some
last minute browsing of notes.
Best advice: Dedicate this fight to the Lord!

TRUST IN THE LORD WITH ALL

YOUR HEART AND LEAN NOT ON
YOUR OWN UNDERSTANDING. IN
ALL YOUR WAYS ACKNOWLEDGE
HIM AND HE SHALL KEEP YOUR
PATH STRAIGHT.
- King Solomon, Proverbs 3:5-6

THANKS FOR LISTENING!

RGO Paragas- 2012