Chapter I: Basics of organic chemistry

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I. Introduction
 Organic chemistry studies carbon and its compounds.
 Carbon forms a huge variety of molecules essential in medicine, agriculture, and
daily life.
I.1. Historically:
o Ancient use of natural organic substances (dyes, medicines, poisons).
o 18th–19th century: isolation of pure compounds, elemental analysis, and
rejection of the “vital force” theory after Wöhler synthesized urea (1828).
o Development of valence theory (1858) and rapid advances in synthesis,
mechanisms, and structural theories.
 Today: organic chemistry also explains biological molecules (proteins, DNA).

I.2. The Carbon Atom

 Definition: Carbon forms covalent bonds with H, O, N, and other nonmetals; bonds
with itself to make chains or rings.
 Nucleus: Contains protons (+) and neutrons (0); electrons (−) orbit outside.
 Structure:
o Atomic number: 6, symbol: C
o Ground-state configuration: 1s² 2s² 2p²
 Orbitals:
o 1s orbital (2 e⁻)
o 2p orbitals (6 e⁻ max; carbon has 2)

I.3. Properties of Carbon

 Ionization energies: 1st = 11.26 eV, 2nd = 24.38 eV, etc.
 Electronegativity: 2.55
 Good electrical (61×10³ S·m⁻¹) and thermal conductivity (129 W·m⁻¹·K⁻¹).
 Isotopes:
o C-12 (99.9%): standard for atomic masses.
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 o C-13 (1.1%): used in NMR, metabolic studies.
o C-14 (trace): radioactive, used in radiocarbon dating.
I.4. Electronic Structure & Hybridization
 Hybridization: mixing of orbitals to form new hybrid orbitals for bonding.
 Fundamental state: 1s² 2s² 2p² → valence = 2
 Excited state: 1s² 2s¹ 2px¹ 2py¹ 2pz¹ → valence = 4
 Quantum numbers:
o n (principal) → shell n (n = 1, 2, 3…)
o l (azimuthal) → orbital shape (s, p, d, f) l (l = 0, 1, 2, ..., n−1)
o m (magnetic) → spatial orientation m (−l ≤ m ≤ +l)
o s (spin) → electron spin (+½, −½)

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I.5. Chemical Bond
 A bond forms when atoms share or transfer electrons, lowering the system’s total
energy.
 Carbon, the basis of organic chemistry, mainly forms covalent bonds.
 The valence shell (outermost shell) is always involved in bonding.

I.5.1. Types of Bonds

I.5.1.1. Ionic Bond
 Formation: Transfer of electrons (metal → nonmetal).
 Example: NaCl.
 Properties: High melting/boiling points, conduct electricity in molten/aqueous state.

I.5.1.2. Covalent Bond

 Formation: Sharing of electrons (usually between nonmetals).
 Types:
o Single (H₂)
o Double (O₂)
o Triple (N₂)

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I.5.1.3. Coordinate covalent bond (dative): both electrons from the same atom.
Properties: Variable melting/boiling points, usually poor conductors.

I.5.1.4. Metallic Bond

 Formation: “Sea of delocalized electrons” around positive metal ions.
 Example: Copper (Cu).
 Properties: High conductivity, malleable, ductile, high melting/boiling points.

I.5.1.5. Polar vs. Nonpolar Covalent Bonds

 Nonpolar: Equal sharing (H₂, O₂).
 Polar: Unequal sharing due to electronegativity difference (H₂O).

I.5.1.6. Hydrogen Bond

 Weaker than ionic/covalent bonds.
 Example: H in water attracted to O of neighboring molecule.
 Significance: Explains many unique properties of water.

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I.5.2. Hybridization of Carbon
Hybridization = mixing of atomic orbitals (s and p) to form new hybrid orbitals that determine
molecular geometry, bond angles, and reactivity.

I.5.2.1. sp³ Hybridization (Tetrahedral)

 Combination: 1s + 3p → 4 sp³ orbitals
 Geometry: Tetrahedral
 Bond angle: 109.5°
 All bonds identical.

 Example: CH₄ (methane)

I.5.2.2. sp² Hybridization (Trigonal Planar)

 Combination: 1s + 2p → 3 sp² orbitals + 1 unhybridized p orbital
 Geometry: Trigonal planar
 Bond angle: ~120°
 Example: C₂H₄ (ethylene, double bond).

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I.5.2.3. sp Hybridization (Linear)
 Combination: 1s + 1p → 2 sp orbitals + 2 unhybridized p orbitals (py, pz)
 Geometry: Linear
 Bond angle: 180°
 Example: C₂H₂ (acetylene, triple bond).

I.6. Structural Formulas

I.6.1. Complete Structural Formula
1. Complete Structural Formula (Lewis Structure)
 Shows all bonds between atoms using dashes:
o Single bond → ―
o Double bond → ═
o Triple bond → ≡
 Example: Methane (C₂H₆), ethane (C₂H₄), propane (C3H8).

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  VSEPR theory explains 3D shapes (e.g., methane = tetrahedral).

I.6.2. Condensed Structural Formula

In condensed structural formulas, the bonds to each carbon are omitted, but each
distinct structural unit (group) is written with subscript numbers designating multiple
substituents, including the hydrogens.
For example, the complete structural formula for ethane, ethene and ethyne is shown as
below:

I.6.3. Bond Line Structural Formula

A bond line structural formula is another way of structural representation of organic
compounds. Here, every bond is represented as a line in a zigzag manner. If not specified,
every terminal is assumed to be a methyl (-CH3) group.

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I.6.4. 3D Representation (Wedge-Dash Notation)
 Used to show molecules in three dimensions:
o Solid wedge (▲): bond coming out of the plane (toward viewer).
o Dashed wedge (▿): bond going back into the plane (away from viewer).
o Line (―): bond in the plane of the paper.
 Example: methane (CH₄) drawn in wedge-dash form.

I.7. Functional Group Classification

Functional Group Classification

 Inorganic chemistry is organized by the periodic table; in organic chemistry, the vast
number of compounds is managed by grouping them into families.
 Functional groups: specific atoms or groups of atoms in molecules that determine
characteristic chemical properties.
 These properties are largely independent of the rest of the molecule, making
classification and study easier.
 The advantage: compounds’ properties and reactivity can be predicted from their
structures.

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  In IUPAC nomenclature, compounds are classified based on the main functional
group, chosen according to a priority system.
 Priority depends on the oxidation state of the central carbon: the higher the
oxidation state, the higher the priority (e.g., carboxylic acids > alcohols).

I.7.1. Functional Groups

1. Carboxylic Acids (highest priority among carbon-containing functional groups).

2. Carboxylic Acids derivatives

3. Other groups containing oxygen or nitrogen

4. Alkenes and Alkynes

Note: substances containing double and triple bonds are called alkenynes. (notice that the
name ends in yne). Chain numbering starts from the end closest to either group, unless they’re
both equidistant from the chain ends, in which case the double bond takes priority and is
given the lower number. See examples in the textbook.

5. Lowest priority: These groups are usually considered substituents in the main chain.

I.7.2. Functional group priorities, highest to lowest

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11
 12. Arene (cyclic of Aryl ene Benzene
arrays of (C=C)

13. (C=C) Alkenyl -ene propene

Alkene

14. (C ≡ C) Alkynyl -yne ethyne

alkyne

15. (C-C) Alkyl -ane methane

Alkane

16. (C-O-C) Alkoxy -ane methoxymethane

Ether

17. R-X Halo- -ane bromomethane

Alkyl halide

18. NO2 Nitro -ane nitromethane

Nitro

II. Nomenclature of Organic Compounds

 Early names of organic compounds were based on origin (e.g., citric acid from citrus fruits)
or properties (e.g., aromatic compounds named for fragrance).
 With the discovery of more compound, especially hydrocarbons, isomerism became
important:
 Isomers: same molecular formula, different bonding/structure.
 Example: C₄H₁₀ → n-butane (straight chain) & isobutane (branched chain).
 Functional groups greatly increase the number of possible compound.
 Random naming was impractical → need for a systematic nomenclature.
 1892 (Geneva): first systematic rules proposed.
 1931: International Union of Chemists (I.U.C.) gave its report → I.U.C. system.
 Later refined by IUPAC (International Union of Pure and Applied Chemistry), which
sets the current widely accepted rules.

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 Nomenclature of organic compounds is based on alkanes.
 Unbranched alkanes = normal (n-) alkanes.
 Homologous series: compounds differing by –CH₂– unit.

II.1. Alkane
Table: IUPAC Names of straight chain alkanes having general formula CnH2n+2

The branched chain alkanes are named by using the following steps:
1. The longest continuous chain of carbon atoms is taken as the parent hydrocarbon. For
example, in the compound shown below, the parent hydrocarbon is heptane and not the
hexane.

2. Identify the substituent alkyl groups attached to the parent chain. Some common alkyl groups
are listed in Table below. You can locate that both the substituents in the example cited above
are methyl groups.
Alkyl group Common name IUPAC name
CH3 methyl methyl
CH3CH2 ethyl ethyl
CH3CH2CH2 n-propyl propyl
Iso-propyl 1-methylethyl

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 CH3CH2CH2CH2- n-butyl butyl
Iso-butyl 2-methylpropyl

Sec-butyl 1-methylpropyl

tert-butyl 1,1-dimethylethyl

neo-pentyl 2,2-dimethylpropyl

3. The parent carbon chain is then numbered in such a way that the substituents get the lowest
possible numbers. The carbon atoms in the above compound can be numbered as:

4. Perfixes di, tri, tetra, penta etc, are used when the substituents occur more than once. Since in
the above compound the methyl substituent is occurring twice, the name is prefixed with di for
the above compound.
5. The name of the compound is written by writing the location and name of the substituents
followed by the name of the parent alkane. Thus, the above compound can be named as 3, 4-
dimethylheptane. Note that a comma is used to separate the two numbers and the numbers are
separated from names of groups by a hyphen. Also note that there is no blank space between
the name of the last substituent and the parent alkane.
6. When more than one type of alkyl groups are present, then they are cited in the name in the
alphabetical order, regardless of their location in the principal chain.

The numerical prefixes di, tri, tetra, etc. and hyphenated prefixes such as sec-tert – are not
considered in determining the alphabetical order but prefixes iso, neo, cyclo are considered for
alphabetizing. To understand it, let us consider the examples given below:

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7. The branched chain substituents, such as 1-methylethyl shown in step 6, are numbered starting
from the carbon attached directly to the parent chain. Note that the name and numbering of
branched substituent is written in brackets in order to separate it from the numbering of the
main chain.

8. The alkyl substituents can be further classified as primary, secondary or tertiary. An alkyl
group is called a primary alkyl group if the carbon atom at the point of attachment is bonded
to only one other carbon. For example, R – CH2 – is a primary alkyl group. Similarly, a
secondary alkyl group has two alkyl groups bonded to the carbon atom taken as the point of
attachment to the main chain. Thus, a secondary alkyl group can be written as shown below:

9. When more than one carbon chains of equal length are available, the numbering is done
considering the following points:
(a) The principal chain should have the greatest number of side chains. For example, in the
compound shown below:

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 The chain having numbering in red color has four side chains while the chain marked
with numbers in black color has three side chains. So the principal chain is the one which is
marked in the red color. Hence, the name is 3-ethyl-2,5,6-trimethyloctane.

(b) The chain having the lowest number for substituents is chosen as the principal chain. In
the compound shown below;

If the numbering is done as shown in black color, the name would have substituents at
positions 3,4 and 5. But, if the carbon chain numbered in red color is taken as the principal
chain, then the substituents get the numbers 2, 3 and 4, which is obviously the correct choice.

II.2. Alkenes
The suffix ane of the parent hydrocarbon is changed to ene and the functional group (a
double bond in this case) is given the lowest possible number.
Their general formula: CnH2n
Some examples are:

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II.3. Alkynes
Alkynes are unsaturated, non-cyclic hydrocarbons that have a carbon-carbon 𝐶 ≡ 𝐶
trible bond.
Their general formula CnH2n-2
The ending ane of the corresponding alkanes is replaced by the ending yne. For the
first compound in this series H−C≡C−H, the trivial name acetylene is used instead of ethyne.
When both double and triple bonds are present, then the double bond gets the lower
number. Thus, for the compound show below.

II.4. Alkyl halides

The alkyl halides are the halogen derivatives of alkanes. The halogens present are
usually F, Cl, Br and 1. The common names are arrived at by writing the name of alkyl group
followed by the name of the halide. Examples are shown below:

In the IUPAC system of nomenclature, prefix halo- (i.e., fluoro, chloro-, bromo or
iodo-) is used to give the lowest number to the carbon atom to which the halogen is attached.
For example, some halogen compounds are named below:

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 When more than one type of halogen atoms are present, their names are arranged in
alphabetical order as shown in the next example,

II.5. Alcohols
The name for an alcohol uses the -ol suffix with the name of the parent alkane,
together with a number to give the location of the hydroxyl group.
-Name the longest carbon chain that contains the carbon atom bearing the ―OH group. Drop
the final -e from the alkane name, and add the suffix -ol.
- Number the longest carbon chain starting at the end nearest the ―OH group, and use the
appropriate number, if necessary, to indicate the position of the ―OH group.
- Name the substituents, and give their numbers as for an alkane or alkene.
- We distinguish:

II.6. Ethers
The common names for ethers are derived by naming the two alkyl groups in
alphabetical order followed by the word ether. This is illustrated in the examples given below:

In the IUPAC system, ethers are named as alkoxyalkanes. The larger of the two alkyl
groups is chosen as the hydrocarbon chain. For example, the compound,

is named as 1-methoxyethane and not as ethoxymethane. Similarly, the compound,

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has the name 1-ethoxy-2-methylpropane.

II.7. Aldehydes
Aldehydes are carbonyl compounds. They have the characteristic group:

Note: Functional carbon is trigonal.

In the IUPAC system of nomenclature, they are named as alkanals. The simplest
aldehyde is methanal. Since the aldehyde group – CHO) is always at the end of the chain, it
is always numbered as C– 1 in the chain, but this number is not specified in the name, i.e. the
compound.

is named as 3, 3-dimethylbutanal.

II.8. Ketones
ketones are carbonyl compounds. They have the characteristic group:

The name of a ketone derives from that of the alkane with the same carbon skeleton,
by replacing the final e by the one ending preceded by the position of the carbonyl group in
the main chain. The functional carbon cannot be at the end of the chain.

Acetone: propanone is used as a solvent (nail polish remover).

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 As usual, the position of the carbonyl group is indicated by the lowest possible

number. A few examples are

II.9. Carboxylic acids

Carboxylic acids have in common the characteristic group: R – COOH

- The functional carbon is trigonal and it is bonded to two oxygen atoms.
the IUPAC names are derived by replacing e ending of the alkane by oic acid. As for
aldehydes, the carboxyl carbon is numbered 1. However, in case of the dicarboxylic acids, the
final e of the hydrocarbon is not dropped.

Ex: dicarboxylic acids

2,3-dihydroxybutanedioic acid (Tartaric acid)

II.10. Acyl halides

Acyl halides are commonly named by placing the names of the halide after the name
of the acyl group. The acyl group is obtained from the carboxylic acid by removal

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 IUPAC names for acyl groups use the ending oyl instead offending e in the name of
the corresponding hydrocarbon. The acetyl chloride has the IUPAC name ethanoyl chloride.
Another example: is named as 2-methylpropanoyl chloride

II.11. Amides
The common names for acid amides are derived by replacing the suffix ic or oic of the
carboxylic acid by the suffix amide. A distinction is made between primary amides, secondary
amides and tertiary amides.

The IUPAC name for an amide is derived by appending the suffix amide to the parent
hydrocarbon with the final e dropped. Thus, acetamide has the IUPAC name ethanamide.
Having done this, can you give common and IUPAC names for

These are formamide and methanamide, respectively.

II.12. Acid anhydrides

A symmetrical anhydride is named as anhydride of the parent acid. Thus,

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 The anhydride which is obtained from ethanic acid (common name: acetic acid) is
commonly known as acetic anhydride. The IUPAC name for this anhydride is ethanoic
anhydride.
For mixed anhydrides, both the parent carboxylic acids are cited in alphabetical order,
followed by the word anhydride, as illustrated below:

Primary amide:

Secondary amide:

N-methylethanamide
Tertiary amide:

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II.13. Esthers
General formula CnH2nO2
The name of the ester derives from that of the alkane of the same carbon skeleton by replacing
the final e by the ending -oate, and its position only at the end of the chain

Esters are chemical species that often have a pleasant smell (rose, jasmine, lavender, etc.).
They are sometimes the source of natural fruity flavors and are very frequently synthesized
for use as food flavorings.

II.14. Amines
There are two systems of naming amines. One method names them as alkylamines and
the other calls them as alkanamines. The alkanamine naming system was introduced by
Chemical Abstracts and
is easier to use as compared to the earlier IUPAC system of alkylamine names. The latest
revision of IUPAC rules accepts both systems and examples below are named in both ways.
A distinction is made between primary amines, secondary amines and tertiary amines.

Bonding, Functional Group Classification and Nomenclature

(Note that the numbering starts at the carbon and not at the nitrogen of the amine part).
Primary diamines are named by using the suffix diamine after the name of the hydrocarbon.

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 For the secondary and the tertiary amines, the longest alkyl group present is
considered as the parent chain. The remaining alkyl groups are named as substituents attached
to the nitrogen and a prefix N- is used with the name of the alkyl group.

When used as a substituent, the – NH2 group is named as amino and is prefixed with a
number indicating the carbon atom to which it is attached.

Nitro compounds: The nitro compounds are named as nitroderivatives of the corresponding
hydrocarbons.
Examples:

II.15. Nitriles
Nitriles are named in the IUPAC system by using the suffix – nitrile to the name of the
hydrocarbon corresponding to the longest carbon chain. Note that here the carbon of the
nitrile group is included in the numbering of carbon chain and is numbered as position 1.
Some examples are given below:

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When named as a substituent, the – CH group is called a cyano group. For example, the
compound.

is named as cyanomethyl ethanoate.

II.16. Thiols
In naming thiols, an ending thiol is used as a suffix to the name of the corresponding
hydrocarbon; for example,

II.17. Sulphonic acids

The names of sulphonic acids use the suffix sulphonic acid with the name of the
corresponding hydrocarbon.

II.18. Some Examples with Multiple Functional Groups

 Monofunctional compounds: contain one functional group.
 Polyfunctional compounds: contain more than one functional group → one is chosen as
the principal group (named as suffix).
 Priority order (decreasing):
Carboxylic acid > Sulphonic acid > Ester > Acid anhydride > Acyl halide > Amide >
Nitrile > Aldehyde > Ketone > Alcohol > Thiol > Amine > Alkyne > Alkene > Ether >
Halide > Nitro.
 Rules for priority:
1. Groups with an IUPAC suffix that terminate a chain (e.g., carboxylic acids) =
highest priority.
2. Groups with a suffix but can occur anywhere in chain (e.g., –OH, –NH₂) = next.
3. Groups with no suffix (treated as substituents, e.g., halogens) = lowest priority.

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 Here are some examples of applying the order of functional group priorities to solve
nomenclature problems. The highest ranked functional group becomes the suffix – it’s
highlighted in red.

(a) Compounds Containing One Aromatic Ring

This class includes benzene and its derivatives. The derivatives of benzene include the
compounds which can have any of the functional groups discussed before attached to the
benzene ring.

(b) Compounds Containing Two Aromatic Rings

Examples being naphthalene and biphenyl.

(c) Compounds Having More Than Two Aromatic Rings

Examples are:

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(d) Heterocyclic Compounds
Aromatic compounds containing heteroatoms such as O, N or S in the aromatic ring
are called heterocyclic compounds. Some heterocyclic compounds are shown below:

(a) Benzene and its Derivatives

A number of monosubstituted benzene derivatives are known by their special names.
These names are in common use for long and hence are approved by IUPAC. Some examples
of these compounds are given below along with their common and IUPAC names (in
brackets).

For disubstituted benzene derivatives, the following three arrangements of the substituents are
possible.

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 These arrangements are named using the Greek prefixes ortho-, meta and para which
are abbreviated as o-, m- and p-. The substituents are then named in the alphabetical order.
This is illustrated in the examples below:

Dimethyl derivatives of benzene are known as xylenes. The three xylenes are;

When one substituent is such that it corresponds to the monosubstituted benzene that
has a special name, then this substituent is called the principal functionality and the compound
is named as a derivative of that parent functionality. For example,

The polysubstituted benzenes are named by identifying the principal functions and
then numbering is done such as to keep the principal function as number. The other
substituents are then given the lowest possible numbers. This is illustrated in the following
examples.

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III. Introduction to Structural Chemistry
III.1. Notions of stereo-isomerism
 Isomers: same molecular formula but different structures → different
physical/chemical properties.
 Two main categories:
1. Constitutional isomers → differ in connectivity of atoms.
2. Stereoisomers → same connectivity but differ in spatial arrangement.
 Geometrical isomers (cis/trans).
 Optical isomers (enantiomers).
 Conformational isomers: arise from rotation around single bonds; usually not
considered under classical isomerism since they are not always separable.

Isomers that differ from the order in which the constituent atoms are connected to each
other are called constitutional isomers. Some examples for constitutional isomers are given in
the table 1.

Constitutional isomers (structural isomers) can be different in their chain structures,

functional groups due to different connectivity of atoms within the molecule. Different

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structural isomers are assigned different IUPAC names. Therefore, constitutional isomers can
be subcategorized into Chain isomers, position isomers and functional group isomers.
III.1.1. Chain (Skeletal) Isomerism
 Definition: Compounds with the same molecular formula but different carbon
skeletons.
 Difference arises from variations in the branching of the carbon chain.
 Results in different physical properties of the isomers.
Ex : C4H10 represents two compounds

It should be mentioned that the isomer which has the most branched structure will
have the lowest boiling point.
Ex : C5H12 represents three compounds

Also, Skeletal isomerism lies between rings and aliphatic (acyclic) alkenes.
Example: C6H12, I = 1 (a double bond or a ring).

III.1.2. Positional isomerism

Compounds having same molecular formula but the position of functional group,
multiple bond or branches along the same chain length of carbon atoms vary.
Ex 1 : C6H5ClOH, I=4.

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Ex 2 : C3H7X

III.1.3. Functional Group Isomerism When isomers have the same molecular formula but
different functional groups, these compounds are called functional group isomers. The
following pairs of families show this isomerism.
Ex : C4H10O

Ex : C3H6O

III.2. Stereoisomerism
III.2.1. Geometrical Isomerism

 Cause: Restricted rotation around C=C double bond (σ + π bond).

 Condition: Each carbon of C=C must carry two different groups.
 Result: Different spatial arrangements → geometrical isomers (not interconvertible
by rotation).
Types:

III.2.1.1. Cis–Trans Isomerism

Cis: similar groups on same side.

Trans: similar groups on opposite sides.

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 Properties:
 Stability: Cis < Trans
 Dipole moment: Cis > Trans (Sym. trans = 0)
 Polarity: Cis > Trans
 Solubility (polar solvents): Cis > Trans
 Boiling point: Cis > Trans
 Melting point: Cis < Trans

III.2.1.2. E–Z Isomerism (general system)

E (entgegen) = high-priority groups opposite.

Z (zusammen) = high-priority groups same side.

Priority rules (Cahn–Ingold–Prelog):

1. Higher atomic number → higher priority.

2. If same → higher atomic mass.

3. If still same → consider next attached atom.

4. Multiple bonds treated as if atoms are duplicated.

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III.2.1.3. Syn–Anti Isomerism (older usage, esp. C=N double bonds)
Syn: –OH and H on same side (or OH with alphabetically first alkyl in
ketoximes).
Anti: –OH and H (or OH and alkyl) on opposite sides.
Essentially corresponds to Z (syn) and E (anti).

Geometrical & Optical Isomerism

1. Geometrical Isomerism in Cyclic Compounds
 No free rotation in rings.
 Cis: substituents on the same side of the ring plane.
 Trans: substituents on opposite sides.

2. Optical Isomerism
 Requires chirality (C atom bonded to 4 different groups = chiral center).
 Chiral molecules → optically active.
 Achiral molecules → optically inactive.
 Non-superimposable mirror images = enantiomers.
Enantiomers:
 Same molecular formula & connectivity.
 Rotate plane-polarized light in opposite directions (+ / – or R/S).
 Can differ in chemical/biological activity (e.g., drugs).

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Diastereomers:
 Stereoisomers that are not mirror images.
 Examples: molecules with multiple chiral centers.
Racemic mixture (racemate):
 50:50 mixture of two enantiomers.
 Optically inactive (rotations cancel).
Absolute & Relative Configuration
1. Configuration
 Absolute configuration: exact 3D arrangement of atoms.
 Relative configuration: compares arrangement to another known compound.

2. Representations of Chiral Molecules

 Wedge-dash diagrams
 Sawhorse formula (cyclic molecules)

 Newman projection (view along C–C bond axis)

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  Fischer projection:
o Vertical = bonds behind plane.
o Horizontal = bonds in front.
o Longest chain vertical; most oxidized group at top.

3. Cahn–Ingold–Prelog (CIP) System (R/S Notation)

 Assign priorities (atomic number → atomic mass → next atom → treat multiple bonds
as repeated atoms).
 Lowest priority group at the back.
 Clockwise (1→2→3) = R (rectus).
 Counterclockwise (1→2→3) = S (sinister).
 Mirror images: R ↔ S.

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4. Chirality without Chiral Centers
 Possible if the molecule as a whole is asymmetric (e.g., allenes like penta-2,3-diene).

5. Molecules with Multiple Chiral Centers

 Maximum stereoisomers = 2ⁿ (n = number of chiral centers).

 Example with 2 centers → 4 stereoisomers: (2S,3S), (2R,3R), (2R,3S), (2S,3R).

6. Meso Compounds
 Have ≥2 stereocenters but contain an internal symmetry plane.
 Mirror halves cancel stereochemistry → optically inactive.

IV. Major reactions in organic chemistry

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1. Reaction Mechanism
 Explains how and why reactions occur.
 Describes the steps from reactants → intermediates → products.
 Considers electronic, geometric, energetic, and kinetic changes.

2. Key Aspects of a Reaction

 Electronic aspect (bond breaking/formation):
o Ionic (heterolytic) → acid/base catalysis.

o Radical (homolytic) → favored by heat or light.

o Molecular (pericyclic) → orbital reorganization (e.g., Diels–Alder).

 Geometric aspect → changes in molecular configuration (stereochemistry).

 Energetic/Kinetic aspect → energy variation & reaction rate.

3. Main Types of Organic Reactions

1. Substitution
2. Addition
3. Elimination
4. Rearrangement (transposition)

V.1. Electronic Aspects of Chemical Reactions

1. Electronic Effects
 Caused by uneven charge distribution in molecules.
 Two main types:
o Inductive effect: transmitted through σ-bonds.
o Mesomeric effect: due to π-electron delocalization.

2. Inductive Effect (I-effect)

 Originates from electronegativity differences.

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  -I effect (attractor) → atoms/groups more electronegative than C (e.g., F, Cl, Br, I, –
NO₂).

Ether Xonium Carbonyle derivative ethylenic Aromatic Nitro

 +I effect (donor) → alkyl groups donate electrons, stabilizing carbocations.

 Effect weakens with distance along the chain.

 Stability: +I stabilizes carbocations, while –I destabilizes them.

3. Mesomeric Effect (M-effect)

 Results from delocalization of π electrons in conjugated systems.

 Propagates without weakening in conjugated chains (e.g., benzene).

 +M (electron-donating): –OH, –OCH₃, –NH₂ (donate via lone pairs).

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  –M (electron-withdrawing): –NO₂, –CN, –C=O, halogens.

VI.2. Reactions in Organic Chemistry

Types of reagents:
 Nucleophiles → electron-pair donors (anions or species with lone pairs). They attack
electron-deficient centers.

 Electrophiles → electron-pair acceptors (cations or electron-deficient molecules).

Reactive intermediates:
1. Carbocations (C⁺): (Electrophiles)
o sp² hybridized, electron-deficient.
o Stability ↑ with donor groups, conjugation (mesomeric effect).
o Destabilized by electron-withdrawing groups.
o Formation favored in polar protic solvents.

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 2. Carbanions (C⁻): (Nucleophiles)
o sp³ hybridized, electron-rich.
o Stability ↑ with electron-withdrawing groups, conjugation.
o Destabilized by electron-donating groups.
o Formation favored in polar aprotic solvents.

3. Radicals (C·):
o Formed by homolytic bond cleavage (heat/irradiation).
o Generally sp² hybridized.
o Stability similar to carbocations.

VI.3. Organic chemistry mechanism

A detailed and stepwise description of pathway by which reactant is converted into product is
called reaction mechanism.
Types of Reaction Mechanism

VI.3. Types of Organic Reactions

1. Addition Reactions (characteristic of multiple bonds)
 Free Radical Addition:
o Follows Markovnikov’s rule (negative part attaches to C with fewer H).

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 o Antimarkovnikov addition occurs with peroxides (Kharasch effect).

o Mechanism: initiation → propagation → termination.

 Chain Initiation Step: Peroxide dissociates into two free radicals called alkoxy radicals.

2) Chain Propagation Step: Bromine radical adds to a double bond, forming a new free
radical with the odd electron on the carbon atom.

Since secondary free radical is more stable than the primary free radical, only the secondary free
radical is formed. The alkyl free radical (secondary free radical) reacts with an HBr molecule to
generate bromine radical.

(3) Chain Termination Step: Termination occurs by any or all of the reactions which use up species
involved in the propagation steps.

 Nucleophilic Addition:
o Seen with polar groups (C=O, C≡N, C=S).
o Nucleophile attacks electron-deficient carbon.
 Electrophilic Addition:
o Step 1: Electrophile adds to π bond → carbocation intermediate.
o Step 2: Nucleophile attacks carbocation.
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 o Examples: addition of Br₂ (color test for alkenes), addition of HX
(Markovnikov’s rule).

2. Substitution Reactions (replacement of one group by another)

 Free Radical Substitution: e.g., halogenation of alkanes.
 Electrophilic Substitution: typical of aromatic compounds (halogenation, nitration,
sulfonation, Friedel–Crafts).

 Nucleophilic Substitution:
o SN1: 2-step, carbocation intermediate, 1st order kinetics, partial racemization,
possible rearrangements.

o SN2: 1-step, concerted, 2nd order kinetics, backside attack → Walden

inversion.

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3. Elimination Reactions (reverse of addition)

 E1 (Unimolecular):
o 2-step via carbocation.
o Regioselectivity: Saytzeff’s rule (more substituted alkene).
o Stereoselectivity: favors E-alkene.

Step 1: The first step is the rate-determining step involving heterolysis of the substrate to
form a carbenium ion intermediate that rapidly loses a β-proton in the second step.

Step 2: The second step involves the fast abstraction of a proton from the adjacent β-carbon
atom giving rise to the formation of the alkene.

 E2 (Bimolecular):
o 1-step, concerted.
o Requires anti-periplanar geometry.
o Rate = k[substrate][base].

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4. Rearrangements (Transpositions)
 Migration of atom/group within the same molecule.
 Types: nucleophilic, electrophilic, radical.
 Carbocation rearrangements: via H⁻ or R⁻ shifts → more stable cations.
 Examples:
o n-propyl → isopropyl carbocation.
o Pinacol rearrangement → ketones.
o Benzylic transposition → α-hydroxy acids.
o Baeyer–Villiger oxidation → ketones → esters.

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