Biological Chemistry
FIRST YEAR ORGANIC CHEMISTRY
Lecture One
Introduction, Nomenclature,
Bonding
Convenor : Dr. Fawaz Aldabbagh
What is Organic
Chemistry?
It is defined as the study of hydrocarbons
(compounds of hydrogen and carbon) and
their derivatives
7 million Organic Compounds
1.5 million Inorganic Compounds
Animal and plant matter, Foods, Pharmaceuticals, Cosmetics,
Fertilizers, Plastics, Petrochemicals, Clothing
Carbon
Why is it the element of life on earth?
Has Four Bonding Electrons
Unique Strong Covalent
Bonds
Strong Single, Double and Triple Bonds
Average Bond Energies (KJ mol-1)
C-C
607
Si-Si 230
C-H
416
Si-H 323
C-N
754
Si-N 470
C-O
336
Si-O 368
O-Si-O = Sand and Rocks
Simplest Organic molecule
Carbon has 4 valence electrons
H
H
H C H
H C H
H
H
Ne
Neon
methane
H
C
Stable Octet required
Covalent Bonding – Atoms Share Electrons
Ionic Bonding – transfer of one or more
electrons from one atom to another to create ions
Li (3) - 1s2, 2s1
F (9) - 1s2, 2s2, 2px2, 2py2, 2pz1
F- - 1s2, 2s2, 2px2, 2py2, 2pz2
Li+ - 1s2, 2s0
Ionic Compound
2
2
6
2 -2e
Mg (12) - 1s , 2s , 2p , 3s
= LiF
Mg2+ - 1s2, 2s2, 2p6, 3s0
Cl- - 1s2, 2s2, 2p6, 2s2, 2p6
Cl (17) - 1s2, 2s2, 2p6, 3s2, 3p5
2
2
6
2
6
Cl
1s
,
2s
,
2p
,
2s
,
2p
+2e
Ionic Compound
= MgCl2
C(6) - 1s2, 2s2, 2px1, 2py1, 2pz0
lowest energy
state
2
1
C(6) - 1s , 2s ,
Excited
state
+
2s
1
2py ,
4 sp3
1
2pz
Hybridization
+
+
2py
1
2px ,
2px
2pz
4 X sp3
Methane is Tetrahedral
0
109.5
H
C H
H
H
Sp3 hybridized carbon
4 equivalent C-H bonds (s-bonds)
All purely single bonds are called s-bonds
Alkanes
CnH2n+2
H
H H
H H H
H C H
H C C H
H C C C H
H
H H
ethane
C2H6
H H H
propane
C3H8
methane
CH4
CH4
H
H
H C C
H
H
H
Ethane
CH3CH3
CH3CH2CH3
Rotation of groups joined
by single bonds does not
usually require lots of
energy
IUPAC-Nomenclature
The ending of all names of
alkanes is ane – remove H = alkyl
H3C
H3C H
CH3CH2
H
CH3CH2CH2 H
CH3CH2CH2CH2 H
R propyl
methyl
ethyl
CH3CH2
CH3CH2CH2
propyl
CH3CH2CH2CH2
R
butyl
butyl
3D – models show that because of the
tetrahedral carbon atoms the chains are
zig-zagged and not at all straight
Constitutional Isomers
H
H3C
C
CH3
CH3
Isobutane
H3C
CH
CH2
CH3
Isopentane
CH3
H3C
C
CH3
CH3
Neopentane
Has the same molecular formula as
butane, C4H10
CH3
Has the same molecular
formula as pentane, C5H12
Have different Physical
Properties, Mpt, Bpt, densities,
indexes of refraction etc
Naming Compounds
2-methylhexane
2-propylheptane 4-ethyl-3-methylhexane
CH3
H3C
C
CH2 C
CH3
2,3,5-trimethylhexane
CH3
CH3
CH3
4-tert-butyloctane or
4-(1,1-dimethylethyl)octane
2,2,4,4-tetramethylpentane
C1-C4 Alkanes
Methane - origins of life. Atmosphere of Jupiter, Saturn,
Uranus and Neptune. Marsh Gas, Cow’s stomach. Coal
Mines and Natural Gas.
Unprocessed Natural Gas contains 50-90% methane, 110% ethane and up to 8% propane and butane.
Methane and Ethane are handled as compressed Gases
Propane and Butane are stored in low pressure cylinders
In liquified forms (Bottled Gas).
All are Colourless, odourless gases, non-toxic – Danger
in inhaling lies in potential suffocation due to a lack of
Oxygen or Explosions when mixed with air.
CH4 + 2 O2
CO2 + 2 H2O + Energy
Combustion