Introduction to Organic Chemistry, Nomenclature, Reaction Mechanism

1. General Organic
Chemistry
Prepared by – Debadatta Mahapatra (MSc Chemistry)

2. • It is one branch in the entire field of chemistry,
which encompasses many classical subdisciplines
including inorganic, physical, and analytical chemistry,
and newer fields such as bioinorganic chemistry,
physical biochemistry, polymer chemistry, and
materials science. Organic chemistry was singled out
as a separate discipline for historical reasons.
Originally, it was thought that compounds in living
things, termed organic compounds, were
fundamentally different from those in nonliving
things, called inorganic compounds. Although we
have known for more than 150 years that this
distinction is artificial, the name organic persists.
Today the term refers to the study of the compounds
that contain carbon, many of which, incidentally, are
found in living organisms.

3. • Drawing Organic Structures
Drawing organic molecules presents
a special challenge. Because they
often contain many atoms, we need
shorthand methods to simplify their
structures. The two main types of
shorthand representations used for
organic compounds are condensed
structures and skeletal structures.

5. • Assume a carbon atom is
located at the junction of any
two lines or at the end of any
line.
• Assume each carbon has
enough hydrogens to make it
tetravalent.
• Draw in all heteroatoms and
the hydrogens directly bonded
to them.

13. Intermolecular Forces
Intermolecular forces are the interactions that exist between molecules. A functional group
determines the type and strength of these interactions.
3.3A Ionic Compounds
Ionic compounds, such as NaCl, contain oppositely charged particles held together by extremely
strong electro static interactions. These ionic interactions are much stronger than the intermolecular
forces present between covalent molecules, so it takes a great deal of energy to separate Oppositely Charged Ions from Each
other.
3.3B Covalent Compounds
Covalent compounds are composed of discrete molecules. The nature of the forces between the
molecules depends on the functional group present. There are three different types of inter actions,
presented here in order of increasing strength:
• van der Waals forces
• dipole–dipole interactions
• hydrogen bonding

20. Kinds of Organic Reactions
Like other compounds, organic molecules undergo acid–base
and oxidation–reduction reactions,
as discussed in Chapters 2 and 4. Organic molecules also
undergo substitution, elimination,
and addition reactions.

25. Bond Breaking and Bond Making
Having now learned how to write and identify some common kinds of organic reactions, we can
turn to a discussion of reaction mechanism.
 • A reaction mechanism is a detailed description of how bonds are broken and formed
as a starting material is converted to a product.
 A reaction mechanism describes the relative order and rate of bond cleavage and formation. It explains
all the known facts about a reaction and accounts for all products formed, and it is subject to
modification or refinement as new details are discovered.
 A reaction can occur either in one step or in a series of steps.

40. 40
Mechanisms and ‘arrow pushing’– it does not have to be complicated.
Most organic reactions can be classified into one of four types:
1) Substitution – replace one group with another, SN2, SN1 etc.
2)Elimination – take something off, E2, E1 etc. Usually, two groups come
off and an alkene is formed!
3) Addition – add something on! Usually you add two groups to an alkene.
4) Rearrangement – make it look difference.
If you understand the mechanisms of these processes then this will greatly
assist your knowledge of organic chemistry.
The following slides will run through the key features of substitution,
elimination and addition reactions.

41. Mechanism and ‘arrow pushing’– Substitution reactions.
This reaction works because the nucleophile (hydroxide) is attracted to the partial positive
charge on the carbon atom. Bromide anion must be displaced because the C atom can only
be surrounded by a maximum of 8 electrons.
The mechanism is illustrated as shown below (this is called an SN2 reaction):
Now lets consider the reaction of bromomethane (methylbromide) with a nucleophile
such as hydroxide anion
H
H
H
HO C + Br
H
H
H
C Br
HO +
H
H
H
HO C + Br
H
H
H
C Br
HO
H
H
H
HO C + Br
H
H
H
C Br
HO
or, if you prefer
Note how the net negative charge moves from left to right in this mechanism (with the arrows)

42. Mechanism and ‘arrow pushing’.
The mechanism is illustrated as shown below (this is called an SN1 reaction):
In some cases (when a hindered halide is used), the reaction proceeds in two steps:
CH3
CH3
CH3
HO C
H3C
H3C
H3C
step 1
C Br HO +
CH3
C
H3C
+ Br
CH3
CH3
C
3
H C CH3
step 2
You will learn more about the mechanisms of substitution reactions next term,
the important thing for now is to understand the mechanism.
CH3
CH3
CH3
HO C
Br
H3C
H3C
H3C
step 1
C Br HO
CH3
C
H3C CH3
CH3
C
3
H C CH3
step 2

43. Nucleophilic substitution reactions – overview:
Why these reactions are important and some examples:
Yes there will be
a counterion, but
it does not
participate in the
mechanism as
drawn

44. Substitution reactions – some definitions.
O O Br
+
H
H
What is the significance of the ‘saturated carbon atom’.
sp3
hybridised carbon
Br
Which leaving groups can be used – what ‘drives’the reaction?
Leaving group
44
X
H
H
+ O O X
+
Key point: Good leaving groups are halides (Cl, Br, I), OSO2R, and other groups
which stabilise a negative charge.

45. Mechanisms of substitutions reactions: SN2
O Br
+
H
H
H
There are two major mechanisms of substitution reactions.
The first is called the SN2 mechanism – Substitution, Nucleophilic, Bimolecular:
What do these three terms mean?
It is a single step mechanism; the nucleophilic adds and the leaving group is simultaneously
displaced in the same step.Aconcerted mechanism.
Br
H
Energy
Bromide
(starting material)
Reaction co-ordinate.
Ether (product)
O
Rate = k [nBuBr][nPrO-]
What happens if I double the concentration of bromide? What if I double the concentration
of bromide and of propoxide?
Transition state

46. someone tells you it is SN2 then they need to be told that they are incorrect!
The transition state for SN2 reactions:
The SN2 mechanism – structure of the transition state.
What does this symbol mean?
Br
O
Br
+
H
H
H
H
O
δ
δBr
O
H
H
C C
σ
* antibonding orbital (empty)
σbonding orbital (full)
C C
Nu:
What ‘shape’do the
groups around this
atom define?
Note partial bonds to nucleophile and leaving group. Nucleophile adds electron density to * antibonding orbital.
*** Key point of nomenclature; it’s SN2 not SN2*** This is important *** If
What is the hybridisation at this C atom?

47. Stereochemical consquences of SN2 reactions:
The SN2 mechanism – What happens at chiral centres:
Br
O
Br
+
H
Me
H
Me
O
δ
δBr
R configuration
H
Me
O
S configuration:
Key concept – inversion of configuration.
*** Key point of nomenclature; INVERSION *** This is important ***