Organic chemistry general of organic chemistry

1.2 The characteristics of the carbon atom* Carbon atoms can be linked with other carbon atoms to form: linear and branched chains, ring structures  single, double or triple bonds.. 1.

ORGANIC CHEMISTRY

Nguyễn Thị Hiển

Department of chemistry

Faculty of Environment science

Vietnam national university of Agriculture

VIETNAM NATIONAL UNIVERSITY OF AGRICULTURE

CHAPTER 1:

GENERAL OF ORGANIC CHEMISTRY

CONTENTS OF CHAPTER 1

1.1 The development of Organic Chemistry

1.2 The characteristics of the Carbon atom

1.3 Chemical bonding in organic chemistry

1.4 Inductive effect

1.5 Classification of organic compounds

1.6 Classification of organic reactions

1.7 Isomerism in organic chemistry

Primary Secondary Tertiary – – – Quaternary

bond - link - connection

1.1 The development of Organic Chemistry

 Every living organism is made of organic chemicals:

food you eat,

medicine you take,

wood, paper, plastics and fibers

that made modern life possible

……….

⚫ The term “organic chemistry” means the chemistry of compounds from living organisms.

⚫ In the past, the difference between organic and inorganic compounds is “vital force”

 organic compounds contained an undefinable “vital force” which was necessary for the synthesis of an organic compound.

Friedrich W Ö hler (1828) : From the pyrolysis of an inorganic compound, NH OCN, 4

synthesized urea (found in urine):

NH 4 -OCN →→→ H 2 N- CO NH - 2

all organic chemicals

Source of Organic compounds

⚫ Organic compounds are

 derived from living organisms

 synthesized in the laboratory

 Medicines, dyes, polymers, plastics, pesticides,

and a host of other organic substances,…

 are all prepared in the laboratory

Carbon is present in all organic compounds

 Organic chemistry is studying of carbon compounds (except CO, CO , M2 2(CO3)n, M(HCO3)n)

1.2 The characteristics of the carbon atom

* Carbon atoms can be linked with other carbon atoms to form:

 linear and branched chains, ring structures

 single, double or triple bonds

Carbon atoms can link with other elements such as hydrogen, oxygen, nitrogen, sulphur, halogen Forming stable bonds

 The number of carbon compounds is very large

1.2 The characteristics of the carbon atom

* The valence of carbon atom in organic compounds is IV

C6 1s22s 2p2 2 in the basic state

1s 2s2 2 2p2

The attractive state

Each carbon atom has 4 bonds with other atoms.

Ex: CH3-CH=CH2; C2H2; CH COOH3

THE VALENCE OF ELEMENTS IN ORGANIC CHEMISTRY

Valence 1 4 3 2

1.2 The characteristics of the carbon atom

* Hybridization of carbon atom

sp3 hybridization

 sp 3 Orbitals in the structure of Methane

How does bonding in organic molecules with tetravalent carbon atoms occur?

The attractive state

C 6 1s 2 2s 2 2p 2 The basic state

1s 2s 2 2 2p 2

1s 2s 2 1 2p 3

sp 3 hybridization

* Hybridization of carbon atom

Methane molecule

When the 4 identical sp 3 orbitals of carbon

overlap with the 1 orbitals of 4 H atoms, s

4 identical C-H σ bonds are formed and

methane results.

Drawing tetrahedral angles of methane:

The wedge is coming out of the paper

and the dashed line is going behind the paper The solid lines are in the plane of the paper.

A space-filling model of

methane would look like

 Each C-H bond in methane has a 438 kJ/mol

and a length of 110 pm

 The bond angle formed by each H-C-H is

109.5 o , the so-called tetrahedral angle.

* Hybridization of carbon atom

sp 2 hybridization

 the two 2p orbitals of the carbon atom are combined with its 2s

orbital

 to form three new orbitals "sp " hybrid orbitals 2

 one unpaired electron in a non-hybridized p orbital.

Ex ethene molecule:

In ethene, H2C=CH2

both C are sp hybridized 2

4 C-H σ bonds are made by the interaction of Csp 2 with 1s orbitals of H.

1 C-C σ bond is made by the interaction of Csp 2 with another Csp 2

The pi-bond is not shown in this picture.

* Hybridization of carbon atom

sp 2 hybridization

* Hybridization of carbon atom

sp hybridization

In the molecule Acetylene (C2H2),

 both carbon atoms will be sp hybridized

and

 have one electron in each of two unhybridized p orbitals.

Ex: axetylene molecule

 Both C are sp hybridized

2 C-H σ bonds are made by the

interaction of C sp with H1s orbitals (see red arrows)

1 C-C σ bond is made by the interaction

of C sp with another C sp orbital (green arrow)

2 C- C  bonds are made by the

interaction of the 2 pairs of C p orbitals (black arrows)

The 3-dimensional model of acetylene is:



 therefore linear

* Hybridization of carbon atom

sp hybridization

 Practice Problem

1.1 Draw a line-bond structure for propene,

CH3CH=CH2; indicate the hybridization of each

carbon and predict the value of each bond angle

1.2 Draw a line-bond structure for 1,3-butadiene,

H2C=CH-CH=CH2; indicate the hybridization of each carbon and predict the value of each bond angle

* Primary, secondary, tertiary and quaternary nomenclature

(Levels of carbon atoms)

Carbon atoms have 4 levels:

+ Primary: bonded to another carbon atom with a single

bond (1 ) O

+ Secondary: bonded to 2 carbon atoms with 2 single

bonds or 1 carbon atom with a double bond (2 ) O

+ Tertiary: bonded to carbon atoms with 3 single bonds

or 1 triple bond or 1 double bond and 1 single bond

(3 O )

+ Quaternary: Carbon atoms bonded to other carbon

atoms with 4 bonds (4 ) O

Convention : the level of a C atom in compounds with

1.3 Chemical bonding in organic chemistry

The octet rule: atoms will be stable with 8 electrons in the

valence shell like noble gases

Covalent Bonds

⚫ When two or more atoms of the same or similar electronegative or close electronegative react to form bonds, a complete transfer of electrons does not occur

 In this case, the atoms achieve noble gas

configuration by sharing electrons

 The covalent bonds formed between

these atoms by sharing their electrons.

Valence Bond Theory

 Valence bond theory describes a chemical bond as the overlap

of atomic orbitals

Ex 1: The hydrogen molecule:

 the 1s orbital of one hydrogen atom overlaps with the 1s orbital of the second hydrogen atom to form a molecular orbital called a sigma bond, σ

H↑ + ↓H → H↑↓ H

Ex 2: The methane molecule: CH4

 the 1s orbital of each hydrogen atom overlaps with 1sp hybrid 3

orbital of the carbon atom to form a molecular orbital called a sigma bond, σ

Characteristics of covalent bonds

 There are 2 kinds of covalent bonds: sigma bond and pi bond.

 The bond axis is the line conecting 2 atomic nuclei.

• Sigma bond ( ): formed by the axis overlap of hybrid obitals together;  hybrid obitals with AOs or AOp; AOs together; AOp together or AOs with AOp.

• Pi bonds ( ) : formed by the boundary overlap of AOp with AOp (or AOp  with AOd).

+ (a): sigma bond:

A hybrid obital overlaps with an AOs.

Characteristics of covalent bonds

+ pi bonds create multiple bonds

a double bond: a sigma bond and a pi bond

a triple bond: a sigma bond and two pi bonds.

 The organic compounds containing

pi bonds are more active than

those only sigma bonds.

Characteristics of covalent bonds

• Bond energy: the energy makes the bond broken.

Question: compare the durability of the link: single, double, triple carbon-carbon.

• Bond length: an optimum distance between nuclei that leads to maximum bond

stability, a distance called the bond length.

The bond energy is larger, the bond length is shorten.

• Bond polarity: the bond X-Y called:

+ a non-polar covalent bond when 0  |X-Y| 0,4

+ a polar covalent bond when 0,4 < |X- Y|  1,7

(X; Yare the electronegativity of X and Y).

The polarity of bonds: in a bond, the atom with larger electronegativity attracts electrons toward it.

Ex: liên kết C-H, C-C : non-polar

liên kết C-O, O-H : polar

C: 2.5

O: 3.5

H: 2.2

1.4 Inductive effect

⚫ When speaking of an atom’s ability to polarize a

bond, we often use the term inductive effect

⚫ The carbon-carbon bond of ethane is completely nonpolar



 at each end of the bond there are two

equivalent metyl groups:

CH 3 – CH 3

But CH 3 - CH 2 -F

⚫ This is not the case with the carbon-carbon bond of

Ethyl fluoride:

 One end of the bond, the one nearer the fluorine

atom, is more positive than the other

 This polarization of the C-C bond results from an

intrinsic electron-attracting ability of the fluorine

(because of electronegativity) that is transmitted through

space and through the single bonds of the molecule

CH3 CH F2



-⚫ Chemists call this shifting of electrons an

inductive effect, denoted I

 The inductive effect here is electron attracting

(or electron withdrawing), denoted I–Ex: - NO2; F; Cl , Br; I; - SO3H; -CN; - OH, -NH2, -CHO, -COOH, groups with multiple bonds

The group's electronegativity is larger, the electron attracting ability is stronger

Ex : -F > -Cl > -Br > -I

⚫ The saturated hydrocarbon radicals donate electrons

(or electron releasing), denoted +I

The saturated hydrocarbon radicals are larger, more

cumbersome; the electron releasing ability is stronger

Ex: t-C4H9 > iso-C3H7 > -C3H7 > -C2H5 > -CH3

Characteristics of Inductive effect

- The inductive effects weaken as the distance from the substituent increase

⚫ in this case, the positive charge that the fluorine imparts to C 1

is greater than that imparted to C 2 because the fluorine is closer

to C 1 .

- The inductive effect only transmits through the single bond chain

of molecules.

 Practice problem

1.4 Compare the polarity of C-Cl bonds in these

compounds:

CH3Cl; C2H5Cl; CH3CH(CH3)Cl;

1.5 Compare the acidity of these acids:

HCOOH; CH COOH; ClCH COOH; Cl3 2 3CCOOH

KEY   Practice problem

1.4 The polarity of C-Cl bonds in these compounds increases as

follows:

CH3-Cl < C2H5-Cl < CH3CH(CH )Cl3

Because alkyl radicals make +I

and +I: CH - < C3 2H5- < i-C3H7

-1.5 The acidity of these acids increases as follows:

CH3COOH < HCOOH < ClCH COOH < Cl2 3CCOOH

+I (CH ) 0 -I(Cl) -I(3 Cl)3

⚫ More than 22 mill organic compounds,



 each has its own unique physical

and chemical properties.

⚫ The organic compounds are classified into

families according to their structural features based on

The carbon skeleton



 alkanes, alkenes, alkynes

and their derivatives



 They are also called aliphatic compounds

b Cyclic or closed chain compounds:



 Rings are made up of only one kind

atoms, (carbon atoms) are called

homocyclic or cabocyclic compounds

⚫ Aliphatic cyclic compounds are called

alicyclic compounds e.g

 Organic compounds containing one or more

fused or isolated benzene rings and their

functinalized derivatives are called benzenoids or aromatic compounds, eg

 benzene, toluene,

naphthalene, anthracene etc.

 Cyclic compounds containing one or

more heteroatoms (usually O, N, S etc)

are called heterocyclic compounds eg

 ethylene oxide, tetrahydrofuran

(THF),

 furan, pyrole etc.

O O

Ethylen oxide tetrahydrofuran (THF)

Functional groups

⚫ It is possible to classify organic compounds by their

reactivity, e.g by so-called functional groups

⚫ According to the functional groups organic compounds

can be divided into:

⚫ alkanes, alkenes, alkynes, arenes, halides, alcohols, etc

The functional groups.

⚫ A functional groups is an atom or a group of atoms

within a larger molecule that has a characteristic

chemical behaviour

⚫ Chemically, a given functional group behaves almost

the same way in every molecule it’s in

 For example, carbon-carbon double bond is the

simplest functional group;

⚫ Functional group with Carbon-carbon multiple

⚫ Functional group with Carbon singly bonded to

⚫ Functional group with a Carbon-oxygen or nitrogen

1.6 Classification of organic reactions

⚫ Organic chemical reactions can be organized either by

⚫ The kinds of organic reactions: broad types 4

❖ additions ❖ eliminations

C C

H H H

reactants

❖ Eliminations

 the opposite of addition reactions,

⚫ occur when a single reactant splits into two products

 The reaction of an alkyl halide with base to yield an acid and an alkene:

❖ Substitution reactions

⚫ When two reactants exchange parts to give two new

products

 the reaction of alkane with chlorine in the presence

of ultraviolet light to yield an alkyl chloride

❖ Rearrangement reactions

⚫ occur when a single reactant undergoes a reorganization

of bonds and atoms to yield a single isomeric product

 the conversion of cis-2-butene into its trans-2-butene

by treatment with an acid catalyst:

 Mechanism of the reaction

⚫ An overall description of how a reaction occurs is called

the reaction mechanism

⚫ A mechanism describes in detail exactly what takes place

at each stage of a chemical transformation:

❖ which bond is broken and in what order

❖ which bonds are formed and in what order,

❖ what the relative rates of the steps are

Nucleophile and Electrophile

A nucleophile is a “nucleus loving” substance and thus

attracted to a positive charge

 A nucleophile has an electron-rich atom and can form a bond by donating an electron pair to an electron-poor

atom

 Nucleophiles often have lone pairs of electrons and are often negatively charged

 Examples: ammonia, :NH , water, H O:, 3 2

hydroxide ion, HO:, and chloride ion, Cl ,

- An electrophile is “electron loving” and thus

attracted to a negative charge

⚫ An electrophile has an electron-poor atom and can form a bond by accepting an electron pair from a

nucleophile

 Examples: acids (H donors), +

alkyl halides, R+-X- and carbonyl compounds, >C+=O-

Radical reactions

Process that involve symmetrical bond breaking

and making are called radical reactions

A radical (often called a “free radical”) is a

chemical species that contains an odd number of

valence electrons and thus has an orbital that

contains only one electron

1.7 Isomerism

 Isomers are compounds with

the same molecular formula but

different structures or different

CH CH2 3

CH3

(2b) (2a)

Structural isomerism (constitutional isomers)

⚫ Carbon chain isomers - The same molecular formula,

the same functional group

- Different the main chain

Structural isomerism

⚫ functional isomers: - The same molecular formula

- Different the functional group

the same the functional groups

- different the position of

functional groups

Butanol Butane-2-ol

2-methylpropane-2-ol and 2-methylpropanol

But-1-ene and but-2-ene

Geometric isomerism

Rotation about the carbon-carbon double bond is restricted

because it involves breaking the pi bond (requires 264 kJ/mol in ethylene)



 They are 2 geometric isomers

2 CH3 groups on the same side of the ring plane.

2 CH groups on opposite 3 sides of the ring plane.



 They are 2 geometric isomers

Geometric isomerism

The conditions for organic compounds have geometric

isomers:

1 Have double bonds or

unstable rings (3 and 4

carbon-ring)

2 Two substituents of

each carbon atom in the

double bond have to be

a  c and b d 

CIP Rules

⚫ Rule 1 Making assignment of priorities to the

atoms or groups directly attached to each carbon

⚫ An atom with a higher atomic number is higher in priority than an atom with a lower atomic number

⚫ The following priority are assigned:

Br(35) > Cl(17) > O(8) > N(7) > C(6) > H(1)