Introduction to Organic Pharmacy

Basics of Organic Pharmacy

1. INTRODUCTION / HISTORIC

2. Organic Pharmacy
Theoriginaldefinitionoforganicchemistrycamefromthe
followingmisconception:
•Organiccompounds:obtainedfromanimal,
vegetablesource.Materialobtainedfromliving
organism(relatedtolifeprocesses)witha
characteristicof“Vitalforce”or“vitalism”
•Inorganiccompounds:obtainedfrommineralsources
•Organicchemistryisthechemistryofthecompoundsof
Carbon.

3. Organic Pharmacy -Historic
Organicchemistryreceivedaboostwhenitwasrealized
thatthesecompoundscouldbetreatedinwayssimilarto
inorganiccompoundsandcouldbecreatedinthe
laboratory.
Beginning of the 19
th
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
Around1816,MichelChevreulstartedastudyonsoap
fromvariousfatsandalkalisanddemonstrateditwas
possibletomakeachemicalchange(which
traditionallycomefromorganicsources).
•1828,FriedrichWöhlerfirstmanufacturedtheorganic
chemicalurea(carbamide),aconstituentofurine,from
theinorganicammoniumcyanateNH4OCN(Wöhle
synthesis).
•Turningpointaboutthe“vitalforce”theory.

5. Organic Pharmacy -Historic
•Lastdecadeofthe19
th
century:pharmaceutical
industry:acetylsalicylicacid(=aspirin)
manufacturestartinGermanybyBayer
1858,FriedrichAugustKekuleandArchibaldScott
Coupersuggestedthattetravalentcarbonatomscould
linktoeachothertoformacarbonlattice,andthatthe
detailedpatternsofatomicbondingcouldbediscerned
byskillfulinterpretationsofappropriatechemical
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. Howrepresentamolecule?
Molecular formula: C4H10
Abbreviated structural formula: CH3CH2CH2CH3
Skeletal formula: C-C bond
H HHH
Structural/displayed formula: H-C-C-C-C-H
H HHH
3D

13. Organic Pharmacy
•Physicalproperties:
•meltingandboilingpoint
•kindofsolventthatthecompoundwilldissolvein
•Chemicalproperties:
•kindofreagentsthatthecompoundwillreactwith
•kindofproductthatwillbeformed
•sloworrapidreaction
•Eachdifferentarrangementofatomscorrespondstoa
differentcompound.
•Eachcompoundshasitsowncharacteristicssetofphysical
andchemicalproperties.

14. Howatomswillbearranged?
Depending on their electronic
configuration

15. Organic Pharmacy
•Theregioninspacewhereanelectronislikelytobe
foundiscalledanorbital(atomicorbital).Twoelectrons
byorbitalwithoppositespin(pairedelectrons)
•Therearedifferentkindsoforbitalswithdifferentsize,
shapeandwhicharedisposedaboutthenucleusin
differentways.
•Thekindoforbitaloccupiesbyanelectrondependsonthe
energyofthiselectron.
•Orbitalaredeterminedbytheelectronicconfigurationof
eachatom

16. Organic Pharmacy
•Generalformula
•Theorbitalatthelowestenergylevelis
1s

17. Organic Pharmacy
2s oneorbitallargerthan1s(higher
energy)
p 3orbitalofequal
energyon
x,y and
zaxes

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

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
Acovalentbondresultfromtheoverlapoftwo
atomicbonds(eachmustcontainasingle
electron)toformabondorbitaloccupiedbya
pairofelectrons(characteristicstrengthand
length).
Example:BeCl2
Be:atomicnumber:4=1s22s2 nounpairedelectrons
Be1s 2s

21. Organic Pharmacy
Example:BeCl2
Be:atomicnumber:4=1s22s2 nounpairedelectrons
Be 1s 2s
Be 1s 2s 2p
differentorbital=differentbonds
Be 1s s p
p
HYBRIDATIONSP

22. Organic Pharmacy
Example:BF3
B:atomicnumber:5=1s22s22p1 oneunpairedelectrons
B 1s 2s 2p
B 1s 2s 2p
HYBRIDATIONSP2
B 1s 2p

23. Organic Pharmacy
CH4
C:atomicnumber:6=1s22s22p2
C1s 2s 2p
TwopossibleboundsbutCtendstooffertwomore
C1s 2s 2p
HYBRIDATIONSP3
C1s

24. Organic Pharmacy
Overlapoforbitalresultsin:
Sigmabond:strongesttypeofcovalentchemicalbond,
cylindricallysymmetrical
Pibond:weakerthansigmabond,morediffusebonds
thanthesigmabonds.

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
Levelofenergy Type of orbital
Outer electron

27. Organic Pharmacy
Atoms are hold together by forces/bondsby 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/bondsby
transferringor 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/bondsby 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
Intermolecularforces:Dipole-dipoleinteraction
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 dipolewhich 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 pointwill 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).
Solubilitywill depend on the polarityof 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 acidis a substance that
give up a proton (H+) and a baseis 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