Al-Farabi Kazakh National University

Higher School of Medicine

Introduction: Fundamentals of the

structure and reactivity of organic
compounds
 LEARNING OUTCOMES
As a result of the lesson you will be able to:

❏ identify the general structural characteristics of organic molecules, in particular, the tetravalent
nature of carbon and the different ways in which it can be expressed;
❏ define functional group - identify the functional groups in organic molecules;
❏ recognize structural (constitutional) isomers and functional group isomers;
❏ write structures of organic molecules in various ways;
❏ classify the organic compounds; name the compounds according to IUPAC system of
nomenclature and also derive their structures from the given names;
❏ draw structural, condensed, and line formulas for simple chemical compounds;
❏ convert any given structural, condensed, or line formula into its corresponding alternative.
❏ types of reactions in organic chemistry
Literature
Organic Chemistry an intermediate text
Robert V. Hoffman
0-19-509618-5
1997
page 1-5, pages 25-27

Органическая химия том 1

В.Ф. Травень
5-94628-068-6
2006
главы с 1 по 8 и глава 12,
стр 33-43, 50-53, 133-141,

Органическая химия том 2

В.Ф. Травень
5-94628-068-6 5-95628-172-0
2006
весь 2 том полезные главы для медиков
Спирты. Стр 11-15. Эфиры. Стр 91- 94 Адьдегиды. Стр 116-124 Карб.кислоты. стр 206-212 Амины. 361-363 Углеводы. Стр 473-494

Organic Chemistry International Student version 10 edition

T.W.Graham Solomons Craig B.Fryhle
978-0-470-52459-6
2011
p. 42 - 79, pages 137 -154,
What are living things made of?

• Guess how many elements your body

is made up of?
• 25 elements make up all living
things
• About 97% of your body’s mass is
made of just 4 elements: oxygen,
carbon, hydrogen, & nitrogen.
• Two other major elements are
phosphorous & sulfur.
Development of Organic
Chemistry as a Science
In the past
…, Chemistry
Chemistry

Organic
Organic Inorganic
Inorganic
compounds
compounds compounds
compounds

obtained from obtained from

living non-living
organisms sources
Development of Organic
Chemistry as a Science
In 1828, Wohler (a German chemist)

(Inorganic (Organic
compound) compound)
Important Differences Between Organic
and Inorganic Compounds
• Bond type
–Organics have covalent bonds
• Electron sharing
–Inorganics usually have ionic bonds
• Electron transfer
• Structure
–Organics
• Molecules
• Nonelectrolytes
–Inorganics
• Three-dimensional crystal structures
• Often water-soluble, dissociating into ions -electrolytes
Important Differences Between Organic and
Inorganic Compounds

• Melting Point & Boiling Point

–Organics have covalent bonds
• Intermolecular forces broken fairly easily
–Inorganics usually have ionic bonds
• Ionic bonds require more energy to break
• Water Solubility
–Organics
• Nonpolar, water insoluble
–Inorganics
• Water-soluble, readily dissociate
Bioorganic chemistry is a chemistry which integrates organic chemistry and
biochemistry.
Bioorganic chemistry involves the study of biological processes using chemical
methods. Organic chemistry methods are used to synthesize biological

molecules and to examine their structure, to investigate biochemical reactions.

Organic chemistry is the study of the compounds of carbon.
The compounds of carbon are the central substances of which all living things on this planet
are made.
Food
clothes
Pharmaceuticals
DNA: the giant molecules that contain all genetic information for a given species.
proteins: blood, muscle, and skin.
enzymes: catalyze the reactions that occur in our bodies.
Classification of organic compounds
1. According to the character of chain of carbon atoms:
 2. According to the functional group:

All organic compounds are grouped into classes based on characteristic features called functional
groups.
A functional group is an atom or a group of atoms within a molecule that serves as a site of
chemical reactivity.
The most important functional groups with the key structural elements and a simple example.

Functional group and its name General structure and name Example

-F, -Cl, -Br, -I (-Hal) R-Hal CH3CH2-Cl

Halogeno Halogenides

-OH R-OH alcohols CH3-OH

Hydroxy group Ar-OH Phenols C6H5-OH

-OR R-O-R C2H5-O-C2H5

Alkoxy group Ethers

-SH R-SH CH3-SH

Mercapto group Thiols
 Functional group and its name General structure and name Example

-SR R-S-R CH3-S-CH3

Alkylthio group Sulfides

-SO3H R-SO3H C6H5-SO3H

Sulfo group Sulfonic acids

-NH2 RNH2, R2NH, R3N CH3NH2, (CH3)2NH, (CH3)3N

Amines
Amino group

-NO2 R-NO2 CH3CH2-NO2

Nitro group Nitro compounds

Carbonyl group (oxo group) Aldehydes CH3-CHO CH3COCH3

Ketones

Carboxylic group R-COOH CH3-COOH

Carboxylic Acids
 The most important element is…
Carbon
• If you take away the water, the rest of the human body is 53%
carbon.
• It may not be the most abundant element in living things, but it
certainly is the most important. At one time, scientists thought
that the chemical reactions that took place inside of living things
could not occur outside of them.
• The carbon molecules were so complex, scientists thought they
must have been made in some unknown way. They called these
carbon compounds organic compounds
 Why is life based on the element carbon?
• There are two important properties of carbon that
make it a suitable element to form the compounds
in living things:
• Firstly, carbon atoms can link together to form
stable chains of great length.
Why is life based on the element carbon?
• Carbon atoms bind
strongly to each other
and form very large
molecules which are
built around this
carbon 'backbone'.
• The covalent bond between two carbon atoms is
strong so that the backbones are stable. In all of
these compounds simple sub-units called monomers
are linked together by condensation reactions.
 Organic chemistry is the chemistry of
carbon compounds.
Carbon is tetravalent; it always form 4 bonds.
Nitrogen is trivalent; it often form 3 bonds
Hydrogen is monovalent; it always form 1 bond

That’s why organic compounds easy represent by lego bricks

Lots of ways to draw this…
3 Types of Carbon Backbones
 Families of Organic Molecules:
Functional Groups
A functional group is defined as an atom or a group of atoms that effectively determines the
chemical properties of an organic compound.
Functional Groups
Case: identify and name the functional groups below
Identify the functional group(s) in the following
compounds:
(a)

Answer
(a) Carbon-carbon double bond ( ) and
chloro group (⎯Cl)
Identify the functional group(s) in the following
compounds:
(b)

Answer
(b) Carbonyl group ( )
Identify the functional group(s) in the following
compounds:
(c)

Answer
(c) Amino group ( ) and carboxyl group ( )
To which homologous series does each of the
following compounds belong?
(a)
(a) Ester

Answer
State whether each of the following pairs of
compounds belongs to the same homologous
series. Explain your answer.
(b)

Answer
(b) Yes, both of them are alcohols.
(a) Name the homologous series of
organic compounds that contain oxygen
atoms in their functional groups.
(a) Alcohol, ether, aldehyde, ketone, Answer
carboxylic acid, ester, acyl halide,
amide and acid anhydride
(c) Identify and name the functional groups in
the following compounds:
(c) ⎯Br (bromo),

(aldehyde),

(acyl chloride),

(carbon-carbon
double bond) groups

Answer
Lots of carbon compounds seem to be isomers. What is
an isomer?
• In organic chemistry, there are many examples of different compounds which have the
same molecular formula as each other,
• But different arrangements (structures) of the atoms in their molecules.
• These are called isomers.
If isomers have the same atoms in them, surely they
have the same properties, so what's the point?
• In fact, these small changes in structure can have significant effects on the properties of
the substance!
• But, it is important to realize that this can have significant effects in a living system.
• One optical isomer of glucose, for example, can be used by a living cell, but the other
isomer cannot.
• This is because the enzyme in the cell which recognizes glucose is sensitive to only one
form.
Isomerism
 STRUCTURAL ISOMERISM - INTRODUCTION

COMPOUNDS HAVE THE SAME MOLECULAR FORMULA

BUT DIFFERENT STRUCTURAL FORMULA
Chain different arrangements of the carbon skeleton
similar chemical properties
slightly different physical properties
more branching = lower boiling point
Positional same carbon skeleton
same functional group
functional group is in a different position
similar chemical properties - slightly different physical properties
Functional Group different functional group
different chemical properties
different physical properties
• Sometimes more than one type of isomerism occurs in the same molecule.
The more carbon atoms there are, the greater the number of possible isomers
 STEREOISOMERISM

Molecules have the SAME MOLECULAR FORMULA but the atoms are
joined to each other in a DIFFERENT SPACIAL ARRANGEMENT - they
occupy a different position in 3-dimensional space.
There are two types...
• GEOMETRICAL ISOMERISM
• OPTICAL ISOMERISM
Chain Isomerism

• Chain isomers of the same compound are very similar.

• There may be small difference in physical properties such as melting or boiling
point due to different strengths of intermolecular bonding.
• Their chemistry is likely to be identical.
 Positional Isomers

• A simple example of isomerism is given by propanol:

• it has the formula C3H8O (or C3H7OH) and two isomers propan-1-ol (n-
propyl alcohol; I) and propan-2-ol (isopropyl alcohol; II)
• Note that the position of the oxygen atom differs between the two: it is
attached to an end carbon in the first isomer, and to the center carbon in
the second.
• The number of possible isomers increases rapidly as the number of atoms
increases; for example the next largest alcohol, named butanol (C 4H10O),
has four different structural isomers.
Positional Isomers

• Positional isomers are also usually similar.

• There are slight physical differences, but the chemical properties are usually very
similar.
• However, occasionally, positional isomers can have quite different properties
 Isomerism
Constitutional Isomers (Structural Isomers) are different
compounds of the same formula. The different structures
from the previous slide for the formula C4H10 is an example of
Constitutional isomers.
 Isomerism
Constitutional Isomers (Structural Isomers) are different
compounds of the same formula. The different structures
from the previous slide for the formula C4H10 is an example of
Constitutional isomers.

How many isomers are there of an alkane containing five

carbons (C5H12)?

Isomer Strategy – Draw Lewis possible different length

chains of carbons atoms connected with a covalent bond.
 Isomerism
Constitutional Isomers (Structural Isomers) are different
compounds of the same formula. The different structures
from the previous slide for the formula C4H10 is an example of
Constitutional isomers.

How many isomers are there of an alkane containing five

carbons (C5H12)?

Isomer Strategy – Draw Lewis possible different length

chains of carbons atoms connected with a covalent bond.
Chains of 5 carbon atoms
H H H H H

H C C C C C H

H H H H H
 Isomerism
Chains of 4 carbon atoms
H H H H

H C C C C H

H HH C HH
H
 Isomerism
Chains of 4 carbon atoms Chains of 3 carbon
atoms H
H H H H HH C H H
H C C C C H H C C C H
H HH C HH HH C HH
H
H
 Isomerism
Chains of 4 carbon atoms Chains of 3 carbon
atoms H
H H H H
HH C H H
H C C C C H
H C C C H
H HH C HH
HH C HH
H
H

There are three isomers of C5H12

 NOT ISOMER IF…

• They have the same name

• If can rotate/flip one to look like the

other
? same
same ?
same?
same?
Types of carbon

1. Primary (1◦) Carbon connected to one carbon atoms.

2. Secondary (2◦) Carbon connected to two carbon atoms.
3. Tertiary (3◦) Carbon connected to three carbon atoms.
4. How many primary, secondary, and tertiary carbons in the
two different structures of C4H10
Types of carbon

1. Primary (1◦) Carbon connected to one carbon atoms.

2. Secondary (2◦) Carbon connected to two carbon atoms.
3. Tertiary (3◦) Carbon connected to three carbon atoms.
4. How many primary, secondary, and tertiary carbons in the
two different structures of C4H10

Primary carbon = ?
Secondary carbon =
Tertiary carbon =
Types of carbon

1. Primary (1◦) Carbon connected to one carbon atoms.

2. Secondary (2◦) Carbon connected to two carbon atoms.
3. Tertiary (3◦) Carbon connected to three carbon atoms.
4. How many primary, secondary, and tertiary carbons in the
two different structures of C4H10

Primary carbon = 2
Secondary carbon = ?
Tertiary carbon =
Types of carbon

1. Primary (1◦) Carbon connected to one carbon atoms.

2. Secondary (2◦) Carbon connected to two carbon atoms.
3. Tertiary (3◦) Carbon connected to three carbon atoms.
4. How many primary, secondary, and tertiary carbons in the
two different structures of C4H10

Primary carbon = 2
Secondary carbon = 2
Tertiary carbon =
Types of carbon

1. Primary (1◦) Carbon connected to one carbon atoms.

2. Secondary (2◦) Carbon connected to two carbon atoms.
3. Tertiary (3◦) Carbon connected to three carbon atoms.
4. How many primary, secondary, and tertiary carbons in the
two different structures of C4H10

Primary carbon = 2
Secondary carbon = 2
Tertiary carbon = ?
 Types of carbon

1. Primary (1◦) Carbon connected to one carbon atoms.

2. Secondary (2◦) Carbon connected to two carbon atoms.
3. Tertiary (3◦) Carbon connected to three carbon atoms.
4. How many primary, secondary, and tertiary carbons in the
two different structures of C4H10

Primary carbon = 2
Secondary carbon = 2
Tertiary carbon = 0
Types of carbon

1. Primary (1◦) Carbon connected to one carbon atoms.

2. Secondary (2◦) Carbon connected to two carbon atoms.
3. Tertiary (3◦) Carbon connected to three carbon atoms.
4. How many primary, secondary, and tertiary carbons in the
two different structures of C4H10

Isobutane C4H10

Primary carbon = ?
Secondary carbon =
Tertiary carbon =
 Types of carbon

1. Primary (1◦) Carbon connected to one carbon atoms.

2. Secondary (2◦) Carbon connected to two carbon atoms.
3. Tertiary (3◦) Carbon connected to three carbon atoms.
4. How many primary, secondary, and tertiary carbons in the
two different structures of C4H10

Isobutane C4H10

Primary carbon = 3
Secondary carbon = ?
Tertiary carbon =
Types of carbon

1. Primary (1◦) Carbon connected to one carbon atoms.

2. Secondary (2◦) Carbon connected to two carbon atoms.
3. Tertiary (3◦) Carbon connected to three carbon atoms.
4. How many primary, secondary, and tertiary carbons in the
two different structures of C4H10

Isobutane C4H10

Primary carbon = 3
Secondary carbon = 0
Tertiary carbon = ?
 Types of carbon

1. Primary (1◦) Carbon connected to one carbon atoms.

2. Secondary (2◦) Carbon connected to two carbon atoms.
3. Tertiary (3◦) Carbon connected to three carbon atoms.
4. How many primary, secondary, and tertiary carbons in the
two different structures of C4H10

Isobutane C4H10

Primary carbon = 3
Secondary carbon = 0
Tertiary carbon = 1
 Nomenclature of organic compounds
In the early days, organic compounds were named from
their sources (common names), e.g.
Limonene (from lemons)
α-pinene (from pine trees)
Penicillin (from the mould penicillum notatum)
Advantages: Short names. Even today this method used
to some extend, e.g. cubane (named after its shape).
Disadvantage: No obvious way of correlating common/
simple name with the structure of molecules.
 Examples
Latin Latin
Hydrocarbon Hydrocarbon H
Roots Roots
Number of Latin Number of Latin n-butane
Carbons Root Carbons Root
1 meth 12 dodec
2 eth 13 tridec H
3 prop 14 tetradec
4 but 15 pentade isobutane
5 pent c H
16 hexadec
6 hex H
17 heptade H H C H
7 hept
c H C C C H
8 oct
18 octadec
9 non H H C H H
19 nonadec
10 dec H
20 eicos
11 undec neopentane
21 unicos
 IUPAC
● a logical systematic approach is needed. To achieve
this aim an internationally recognized system of
nomenclature devised by the International Union
of Pure & Applied Chemistry (IUPAC) was used.

● Advantages: Knowing the rules for naming, one can

determine the correct structure.
● Disadvantage: Can be cumbersome; e.g. IUPAC name
for cubane pentacyclo[4.2.0.02,5.03,8.04,7]octane
 Systematic System of Nomenclature (IUPAC)

•Find the longest continuous chain of carbon atoms.

•Use a Latin root corresponding to the number of carbons in the
longest chain of carbons.
•Follow the root with the suffix of “ane” for alkanes
•Carbon atoms not included in the chain are named as
substituents preceding the root name with Latin root followed
by “yl” suffix.
•Number the carbons, starting closest to the first branch.
•Name the substituent's attached to the chain, using the carbon
number as the locator in alphabetical order.
•Use di-, tri-, etc., for multiples of same substituent.
•If there are two possible chains with the same number of
carbons, use the chain with the most substituent's.
 ·A chemical name has three parts in the IUPAC system:

Prefix-Parent-Suffix
Where are the substituents? What family?
How many carbons?

● Longest chain with the functional group of the highest priority (principal
functional group)

-COOH, -SO3H, -COOM, -COOR, -CONR2, -CN, -CHO, -CO-, -OH, -SH, NH2,

Decreasing priority of functional groups

 NOMENCLATURE
Common system
Examples
1. Give a name for the following compound

Step #1, count the number of carbons and write down the memorized Latin
name for that number (next slide)
Step #2, since this structure fits the alkane general formula, use the “ane” suffix

propane Alkane suffix

Three carbon Latin root

Substituent Names (Alkyl groups)
Systematic Nomenclature continued.

Which one?
Systematic Nomenclature continued.

Which one?

The one with the most

number of substituent's
Systematic Nomenclature continued.

Which one?

The one with the least

number of substituent's

The top structure has

four substituent's and
the bottom has three
substituent's.
 Systematic Nomenclature continued.

Which one?

The one with the least

number of substituent's

The top structure has

four substituent's and
the bottom has three
substituent's.

Name = ?
 Systematic Nomenclature continued.

Which one?

The one with the most

number of substituent's

The top structure has

four substituent's and
the bottom has three
substituent's.

Name = ? heptane
 Systematic Nomenclature continued.

Which one?

The one with the least

number of substituent's

The top structure has

four substituent's and
the bottom has three
substituent's.

Name = 3,3,5-trimethyl-4-propylheptane
Another Example:

Name = 3-ethyl-2,6-dimethylheptane
Another Example:

Name = 3-ethyl-2,6-dimethylheptane

Notice substituent's are in alphabetical order; di, tri, etc. do

not participate in the alphabetical order
Line Structures
A quicker way to write structures'

(Condensed Structure)

ethy methyl
l
(A line structure of the above
condensed structure)

methyl
Complex Substituent's

•If the branch has a branch, number the carbons from the point of
attachment.
•Name the branch off the branch using a locator number.
•Parentheses are used around the complex branch name.

3
1 1
2

1-methyl-3-(1,2-dimethylpropyl)cyclohexane
• How about C5H12? The isomers are:

Pentane 2-methyl-butane 2,2-dimethyl propane

Nomenclature Practice
Name this
compound

1 9 carbons =
2 3 4 5 nonane
6
7
8
9

Step #1: For a branched hydrocarbon, the longest

continuous chain of carbon atoms gives the root
name for the hydrocarbon
 Nomenclature Practice
Name this
compound

1 9 carbons =
2 3 4 5 nonane
6 CH3 =
7 methyl
8 chlorine =
chloro
9

Step #2: When alkane groups appear as substituents, they are named
by dropping the -ane and adding -yl.
Nomenclature Practice
Name this
compound

1 9 carbons =
2 3 4 5 nonane
6 CH3 =
7 methyl
8 chlorine =
chloro
9
1 9 NOT 9 1

Step #3: The positions of substituent groups are

specified by numbering the longest chain of
carbon atoms sequentially, starting at the end
closest to the branching.
 Nomenclature Practice
Name this
compound

1 9 carbons =
2 3 4 5 nonane
6 CH3 =
7 methyl
8 chlorine =
chloro
9

2-chloro-3,6-
dimethylnonane

Step #4: The location and name of each substituent are

followed by the root alkane name. The substituents
are listed in alphabetical order (irrespective of any
prefix), and the prefixes di-, tri-, etc. are used to
indicate multiple identical substituents.
Naming Practice!!!

choose the correct ending

ene
determine the longest carbon chain with
the double bond
ene
assign numbers to each carbon
ene
assign numbers to each carbon
ene
attach prefix (according to # of carbons)
1-hexene
ene
ethyl

methyl
methyl
determine name for side chains
1-hexene
 ethyl

methyl
methyl
attach name of branches alphabetically
2-ethyl-4-methyl-4-methyl-1-hexene
 ethyl

methyl
methyl
group similar branches
2-ethyl-4-methyl-4-methyl-1-hexene
 ethyl

methyl
methyl
group similar branches
2-ethyl-4,4-dimethyl-1-hexene
or 2-ethyl-4,4-dimethyl hex-1-ene
propene

2,4-dimethyl-2-pentene
2-butene 2,4-dimethyl pent-2-tene
a) 3,3-dimethyl-1-pentene b) same

CH3

CH3 C C CH CH CH3

CH3
c) 4,5 dimethyl-2-hexene