Organic chemistry is the study of carbon-based compounds. Historically, organic compounds were thought to only come from living organisms, but it was discovered they could be synthesized in the lab from inorganic precursors. The structure of organic molecules is based on how carbon atoms bond together, often forming chains, rings, and complex structures. Organic compounds have a variety of applications including in drugs, plastics, food, and living organisms themselves which are mostly composed of organic matter.

1. INTRODUCTION / HISTORIC

2. Organic Pharmacy
The original definition of organic chemistry came from the
following misconception:
• Organic compounds: obtained from animal,
vegetable source. Material obtained from living
organism (related to life processes) with a
characteristic of “Vital force” or “vitalism”
• Inorganic compounds: obtained from mineral sources
• Organic chemistry is the chemistry of the compounds of
Carbon.

3. Organic Pharmacy - Historic
Organic chemistry received a boost when it was realized
that these compounds could be treated in ways similar to
inorganic compounds and could be created in the
laboratory.
Beginning of the 19th century: investigations focused on
inorganic compounds: more promising due to complexity
of organic compounds.
Artificial synthesis of organic compounds from non-
living things seems impossible.

4. Organic Pharmacy - Historic
Around 1816, Michel Chevreul started a study on soap
from various fats and alkalis and demonstrated it was
possible to make a chemical change (which
traditionally come from organic sources).
• 1828, Friedrich Wöhler first manufactured the organic
chemical urea (carbamide), a constituent of urine, from
the inorganic ammonium cyanate NH4OCN(Wöhle
synthesis).
• Turning point about the “vital force” theory.

5. Organic Pharmacy - Historic
• Last decade of the 19th century: pharmaceutical
industry: acetylsalicylic acid (=aspirin)
manufacture start in Germany by Bayer
1858, Friedrich August Kekule and Archibald Scott
Couper suggested that tetravalent carbon atoms could
link to each other to form a carbon lattice, and that the
detailed patterns of atomic bonding could be discerned
by skillful interpretations of appropriate chemical
reactions.

6.  What is so special about the compounds of
carbon that we separate it from the other
element of the periodic table?
So many compounds of carbon and
their molecules can be so large and
complex.
Organic chemistry is based on
structural theory which separate all organic
compound in families

7. DEFINITION / APPLICATION

8. Organic Pharmacy
Organic chemistry is a discipline which involves the
scientific study of:
Structure, properties, composition, reaction and
preparation of chemical compounds consisting
primarily of carbon and hydrogen and which may
contains other elements including nitrogen, oxygen,
halogens as well as phosphorus, silicon and sulfur.

9. Organic Pharmacy
Multiple application:
Chemistry of dyes and drugs, paper and
ink, paints and plastics, gasoline and
rubber tires.
It’s the chemistry of the food we eat and
the clothing we wear.
It’s fundamental to biology and
medicine: living organisms are mostly
made up of organic compounds.

10. ATOMS AND MOLECULES PROPERTIES

11. Organic Pharmacy

12. How represent a molecule?
Molecular formula: C4H10
Abbreviated structural formula: CH3CH2CH2CH3
Skeletal formula: C-C bond
H H H H
Structural/displayed formula: H-C-C-C-C-H
H H H H
3D

13. Organic Pharmacy
• Physical properties:
• melting and boiling point
• kind of solvent that the compound will dissolve in
• Chemical properties:
• kind of reagents that the compound will react with
• kind of product that will be formed
• slow or rapid reaction
• Each different arrangement of atoms corresponds to a
different compound.
• Each compounds has its own characteristics set of physical
and chemical properties.

14. How atoms will be arranged?
Depending on their electronic
configuration

15. Organic Pharmacy
• The region in space where an electron is likely to be
found is called an orbital (atomic orbital). Two electrons
by orbital with opposite spin (paired electrons)
• There are different kinds of orbitals with different size,
shape and which are disposed about the nucleus in
different ways.
• The kind of orbital occupies by an electron depends on the
energy of this electron.
• Orbital are determined by the electronic configuration of
each atom

16. Organic Pharmacy
• General formula
• The orbital at the lowest energy level is
1s

17. Organic Pharmacy
2s one orbital larger than 1s (higher
energy)
p 3 orbital of equal
energy on
x, y and
z axes

18. Organic Pharmacy
s=one orbital, p=3 orbitals, d=5 orbitals

19. 1s
H 2p
He 2s
Li
Be
B
C
N
O
F
Ne
Pauli exclusion principle: only 2 electrons can occupy any
atomic orbital. They must have opposite spins (paired
electrons)

20. Organic Pharmacy
A covalent bond result from the overlap of two
atomic bonds (each must contain a single
electron) to form a bond orbital occupied by a
pair of electrons (characteristic strength and
length).
Example: BeCl2
Be: atomic number: 4 = 1s22s2 no unpaired electrons
Be 1s 2s

21. Organic Pharmacy
Example: BeCl2
Be: atomic number: 4 = 1s22s2 no unpaired electrons
Be 1s 2s
Be 1s 2s 2p
different orbital = different bonds
Be 1s s p
p
HYBRIDATION SP

22. Organic Pharmacy
Example: BF3
B: atomic number: 5 = 1s22s22p1 one unpaired electrons
B 1s 2s 2p
B 1s 2s 2p
HYBRIDATION SP2
B 1s 2p

23. Organic Pharmacy
CH4
C: atomic number: 6 = 1s22s22p2
C 1s 2s 2p
Two possible bounds but C tends to offer two more
C 1s 2s 2p
HYBRIDATION SP3
C 1s

24. Organic Pharmacy
Overlap of orbital results in:
Sigma bond: strongest type of covalent chemical bond,
cylindrically symmetrical
Pi bond: weaker than sigma bond, more diffuse bonds
than the sigma bonds.

25. Organic Pharmacy
Simplified periodic table
S block: outer electrons will be on s orbital (2 electron max)
P block: outer electron will be on p orbitals (3 orbitals/2 electrons, total 6 electrons
max)
PERIODG
R
O
U
P
Electronic configuration determination

26. Organic Pharmacy
Electronic configuration determination
Na: atomic number: 11
Electronic configuration: 3 s 1
Third period S block first group
Level of energy Type of orbital Outer electron

27. Organic Pharmacy
Atoms are hold together by forces/bonds by sharing
or transferring electrons.
Covalent bonds (share of electron) is typical of the
compounds of carbon
H
H C H
H

28. Organic Pharmacy
Atoms are hold together by forces/bonds by
transferring or sharing electrons.
Ionic bonds (transfer of electron), typical of the salts.
Combination of electropositive elements (metallic) with
electronegative elements (non-metallic).
K K+ + e-
Br + e- Br-

29.  It represents the tendency of an atom to
attract electron
 A covalent bond can be polar if joined
atoms have different electronegativity
 The greater the difference in
electronegativity, the more polar the bond
will be.
 Most electronegative element are in the
upper right hand corner of the periodic
table:
F > O > Cl,N > Br > C, H

30. Organic Pharmacy
Atoms are hold together by forces/bonds by sharing
or transferring electrons.
Each bond will be characterized by properties to obtain a
stable configuration/structure:
-strength, length, angle and energy
-association of repulsive (same charge or same spin if
unpaired) and attractive forces (electrons/atomic nuclei)
-polarity due to a non equal share of electron
(electronegativity): with a delta plus and delta minus pole
which indicate a partial + and – charge. (polar molecule
with dipole moment)

31. Organic Pharmacy
Intermolecular forces: Dipole-dipole interaction
Attraction between:
Positive end of one polar molecule and the negative end of
another polar molecule
Hydrogen bonding (strong; with F,O,N):
H-F---H-F H-O---H-O
H H
+ - + -

32. Organic Pharmacy
Intermolecular forces for non-polar molecule: Van
der Walls forces (weak)
Due to the average distribution of charge.
Momentaly, induced dipole which result in attraction

33. Organic Pharmacy
Bond dissociation energy
The amount of energy consumed or liberated when
a bond is broken or formed is known as the Bond
dissociation energy (ΔH).

34.  Melting point
 Boiling point
 Solubility

35. Organic Pharmacy
Physical properties of a compound largely depends of
the characteristics of the bonds that holds atoms in
a molecule.
Melting point will be different for ionic compound (very
high temperature) and non-ionic due to the different bonds
to be broken.
Boiling point (same situation than melting point).
Solubility will depend on the polarity of the compound,
interionic and intermolecular forces to be replaced by
forces between the solvent and the solute.

36.  Acidity & Basicity
 Isomerism

37. Organic Pharmacy
From Lowry-Bronsted: an acid is a substance that
give up a proton (H+) and a base is a substance
that accepts a proton.
From Lewis, an acid is an electron-pair acceptor
and a base is an electron-pair donor.
A proton is an acid due to his lack in electron

38. Acidity increase as electronegativity
H-CH3 < H-NH2 < H-OH < H-F
H-SH < H-Cl
Acidity increase as size
H-F < H-Cl < H-Br < H-I
The degree of acidity depends on the
electronegativity and the size of the atom that
holds the hydrogen.
Organic Pharmacy

39. The different molecular structure conducts to different
compounds with different properties: isomerism
Organic Pharmacy
Constitutional isomers:
Molecular formula: C2H6O
Dimethyl ether
Ethyl alcohol

40. Constitutional isomers (structural isomers) differ in the
connectivity of bonds, whereas stereoisomers have the same
bond connectivities but have bonds oriented differently