BIOCHEM: Module 1 halides

1.1

ORGANIC CHEMISTRY 5. do not ionize in ionizes in

Ionization solution solution
 The study of the compounds of carbon
with the exception of carbon
6. Acidity/
monoxide, carbon dioxide, carbonates
alkalinity low degree high degree
group, and the cyanide group. Even
though these compounds contain
carbon, they have to be bonded with
hydrogen(hydrocarbon). 7.Chemical
Complex simple
structure
HISTORICAL DEVELOPMENT
8.Bond Covalent ionic
 Prehistoric times ancient- Romans,
Egyptians and the Phoenicians used
dyes, which were pure compounds 9. in molten
good conductor
isolated from plant and animal sources. Conductivity state or
of electricity
 They converted animal fat into soap solution
and fermented sugars to yield alcohol.
 Swedish chemist Torbern Bergman was
10.
the first person to express the difference
Isomerism High rare
between organic and inorganic
substance

DIFFERENCE BETWEEN ORGANIC AND  Friedrich Wohler found that it was

INORGANIC COMPOUNDS: possible to convert the organic salt
ammonium cyanate into urea,
Organic Inorganic an organic compound isolated from
Compounds Compounds urine

KOCN + NH4Cl → NH4O

1.Solubility in CN + KCl
soluble in organic
water soluble
solvents
Heat

NH4OCN → NH2 - C- NH2

2. Melting
and Boiling lower higher II
point O

3. Stability  Kolbe synthesized acetic acid from the

less stable stable elements
towards heat
 Berthelot synthesized methane
 August Kekule (Germany)
4. mostly usually not and Archibald Couper ( Scotland) were
Combustion flammable flammable the first to recognize that in all organic
except organic
 compounds, carbon has four “ affinity
units”, said to be tetravalent.
 Jacobus Van Hoff and Joseph Le
Bel proposed that the bonds of carbon
are not randomly oriented but have a
special spatial orientation.
 In 1826 Michael Faraday discovered
benzene, but its structure remained a
mystery for about 40 years. Its molecular
formula C6H6 indicated an unsaturated
hydrocarbon, but did not behave as
alkenes or alkynes.
 1865, August Kekule, a German
chemist, proposed a ring of six carbon
atoms joined alternating single and
double bonds with one hydrogen atom
bonded to each carbon.
SOURCE OF ORGANIC COMPOUNDS
1. Natural sources
1.1 Plants: starch, sugar, cellulose, fibers,
and oils especially waxy varieties of plants
are known to be sources of high
molecular weight alkanes.
 Quinine from bark of cinchona tree
 malic acid from apples
 alkanes and cycloakenes like rubber
turpentine, essential oils and colored
plant pigments.
2.2 Animals : fats, protein and amino acids
 cholesterol from gallstones
 urea form the liver
2. Natural Gas and Petroleum: products
from the underground decay of animals,
plants and marine residues.
2.1 Natural gas: composed largely of
methane and smaller amounts of ethane,
propane and butane
Fractional distillation
gasoline, kerosene, lubricating oils
Petroleum
Paraffin, petroleum ether, tar
1. Coal: one of the major sources of
aromatic hydrocarbon
Destructive distillation: Coal
Fractional distillation: coal tar
Benzene, naphthalene, phenol
2. Fermentation: process of enzymatically
controlled anaerobic breakdown of
energy- rich compounds.
Enzyme
CHO alcohol +carbon dioxide
(Carbohydrates)
3. Laboratory synthesis
Calcium carbide + water
CaC2 + 2H2O
Acetylene + calcium hydroxide
C2H2 Ca ( OH)2
(ethyne)
VERSATILITY AND UNIQUENESS OF CARBON:
1. Carbon is very versatile element; atoms
can unite with one another by sharing
one or more pairs of electron to form
chains, both branches and
unbranched, or ring .
2. Carbon atoms have four valence
electrons so it always form 4 covalent
bonds.
3. Organic molecules exhibit isomerism.
Even the and same number kind of
atoms are present , different organic
compounds can be formed if the
arrangement of these atoms are
changed.
REASON WHY CARBON FORM SO MANY
COMPOUNDS
 Carbon has the ability to bond with
itself to form long chains and ring
structures; hence it can form molecules
that contain from one to an infinite
number of C atoms.
1.3 Hydrocarbons
VERSATILITY AND UNIQUENESS OF CARBON:
1. Carbon is very versatile element; atoms
can unite with one another by sharing
one or more pairs of electron to form
chains, both branches and
unbranched, or ring .
2. Carbon atoms have four valence
electrons so it always form 4 covalent
bonds.
3. Organic molecules exhibit isomerism.
Even the and same number kind of
atoms are present, different organic
compounds can be formed if the
arrangement of these atoms are
changed.
REASON WHY CARBON FORM SO MANY
COMPOUNDS
 Carbon has the ability to bond with
itself to form long chains and ring
structures; hence it can form molecules
that contain from one to an infinite
number of C atoms.
NOMENCLATURE
 System of naming compounds
 Organic compounds are named
according to rules established by the
International Union of Pure and Applied
Chemistry (IUPAC).
THE RULES OF THE SYSTEM ARE AS FOLLOWS:
IUPAC RULES IN NAMING HYDROCARBONS
 Hydrocarbon names are based
on: a) type, b) Number of
carbons, c) side chain type and
position
THE NAME OF EVERY ORGANIC MOLECULE
HAS THREE PARTS:
a. The parent name indicates the number
of carbons in the longest continuous chain.
b. The suffix indicates what functional
group is present.
c. The prefix tells us the identity, location,
and number of substituents attached to
the carbon chain.
CLASSIFICATION OF HYDROCARBONS
A. ALIPHATIC HYDROCARBONS -
compound is a hydrocarbon compound
containing carbon and hydrogen joined
together in straight chains, branched trains
or non-aromatic rings. Aliphatic
compounds may be saturated (e.g.,
hexane and other alkanes) or unsaturated
(e.g., hexene and other alkenes, as well as
alkynes)
IUPAC RULES IN NAMING ALIPHATIC
HYDROCARBONS (ALKANES,ALKENES AND
ALKYNES)
Before we can follow the I .U.P.A.C
rules for naming branched-chain
hydrocarbons, we must consider the
names of the groups that are formed when
one hydrogen atom is removed from the
formula of an alkane. They are called alkyl
groups.
Methane Methyl - CH3
Ethane Ethyl -CH2CH3
 4. Number the chain so that the lowest
n-propane n-propyl - CH2CH2CH3 possible numbers are assigned to the
substituent positions.
- 5. Use commas between substituent
n- butane n- butyl numbers and hyphens between
CH2CH2CH2CH2
numbers and prefixes.
6. Arranged the substituents in
1. Identify the longest continuous carbon alphabetical order.
chain and name the parent chain by
using the appropriate Greek prefix that a. SATURATED HC - stable
would correspond to the number of
carbon atoms in the sequence, to be e.g.
followed by the suffix –ane/ -ene/ -yne. CH3
1 2 3 4 5 6 7
1 – meth 10 – dec 19 – CH3 CH CH CH
nonadec CH2CH2CH3
2 – eth 11 – undec 20 – eicos
3 – prop 12 – dodec 21 – henicos CH3 CH2 -CH3
4 – but 13 – tridec 22 – docos IUPAC Name: 4 – ethyl – 2 – 3 –
5 – pent 14 – 23 – tricos dimethylheptane
tetradec
6 – hex 15 – 24 –
pentadec tetracos b. UNSATURATED HC
7 – hept 16 – 30 – tricont
hexadec 7. In alkenes and alkynes, number the
31 – chain beginning at the end closest to
hebtriacont the double or triple bond.- ene for
alkene.
32 –
dotriacont - yne for alkyne
8 – oct 17 – 40 –
heptadec tetracont Example:
7 6 5 4 3 2 1
50 –
petacont CH3- CH2 – CH2 – CH2 – CH = CH - CH3
9 – non 18 – 100 - hect
octadec 2- heptane
In a compound containing two double
2. Identify the substituent, branch of bonds, the ending – diene is used.
functional group attached to the
parent chain. 1 2 3 4 5 6
3. Use appropriate prefixes to indicate
CH3 - CH = C = CH- CH2 – CH3
more than one of a particular
substituent or branch. e.g. di,tri, 2, 3- hexadiene

tetra, etc.
1 2 3 4 5 6 7 8 9
 CH3 – C=C-C= C-C=C-CH2 -CH3
2,4,6- nonatriyne
1. ALICYCLIC HYDROCARBONS
 Aliphatic compounds containing rings
a. CYCLOALKANES ARE
SATURATED hydrocarbons in which the
carbon atoms form a ring. The general
formula is CnH2n. They are identified by the
prefix cylo___First Four Members of Cyclo
alkane Series
IUPAC RULES FOR CYCLOALKANE
NOMENCLATURE
1.For a monosubstituted cycloalkane the
ring supplies the root name and the
substituent group is named as usual. A
location number is unnecessary.
2. If the alkyl substituent is large and/or
complex, the ring may be named as a
substituent group on an alkane.
3. If two different substituents are present
on the ring, they are listed in alphabetical
order, and the first cited substituent is
assigned to carbon #1. The numbering of
ring carbons then continues in a direction
(clockwise or counter-clockwise) that
affords the second substituent the lower
possible location number.
4. If several substituents are present on the
ring, they are listed in alphabetical order.
Location numbers are assigned to the
substituents so that one of them is at
carbon #1 and the other locations have
the lowest possible numbers, counting in
either a clockwise or counter-clockwise
direction.
5. The name is assembled, listing groups in
alphabetical order and giving each group
(if there are two or more) a location
number. The prefixes di, tri, tetra etc., used
to designate several groups of the same
kind, are not considered when
alphabetizing.
b. CYCLOALKENES
 CYCLOALKENESARE UNSATURATED,
Cyclopro Cyclob cyclope Cycloh
pane utane ntane exane
Molecu
lar
formula C3H6 C4H8 C5H10 C6H12
Conde
nsed
structur
al
formula
alkenes that consist of three or more
carbon atoms linked together with at
least one carbon-carbon double bond
to form a structural ring (hence the
prefix 'cyclo-')
IUPAC RULES FOR ALKENE AND
CYCLOALKENE NOMENCLATURE
1.The ene suffix (ending) indicates an
alkene or cycloalkene.
2. The longest chain chosen for the root
name must include both carbon atoms of
the double bond.
3. The root chain must be numbered from
the end nearest a double bond carbon
atom. If the double bond is in the center of
the chain, the nearest substituent rule is
used to determine the end where
numbering starts.
4. The smaller of the two numbers
designating the carbon atoms of the
double bond is used as the double bond
locator. If more than one double bond is
present the compound is named as a
diene, triene or equivalent prefix indicating
the number of double bonds, and each
double bond is assigned a locator number.
5. In cycloalkenes the double bond
carbons are assigned ring locations #1 and IUPAC RULES IN NOMENCLATURE OF THE
#2. Which of the two is #1 may be ALKYL DERIVATIVES OF BENZENE
determined by the nearest substituent rule.
 When the hydrogen atom in benzene is
replaced with alkyl groups, this gives rise
to numerous other hydrocarbons. The
simplest member is methyl benzene,
commonly called toluene.
 If two hydrogen are replaced by methyl
groups, three different dimethyl
benzenes (commonly called xylene)
can be formed.
1,3-
Cyclohexene is a Cyclopentadiene Note that the location of second
hydrocarbon with the The compound is substituent relative to the first I s indicated
formula C₆H₁₀. This mainly used for the by numbering the ring carbons.
cycloalkene is a production of
colorless liquid with a  Prefixes ortho(o), meta (m) and para
cyclopentene and
sharp smell. It is an (p) are often used if there are two
its derivatives. It is
intermediate in substituent.
popularly used as a
various industrial precursor to  For more than two substituents, numbers
processes may be used. Note also just in the
the cyclopentadien
following structures, it is immaterial
yl ligand (Cp)
whether the symmetrical and all
in cyclopentadienyl
positions are equivalent. However, the
complexes in
numbers are arranged to give the
organometallic
lowest possible numbers to the
chemistry
substituents.

1. ARENE /AROMATIC HYDROCARBONS

 An aromatic hydrocarbonor arene (or

sometimes aryl hydrocarbon) is
a hydrocarbon with sigma bonds and
delocalized pi electrons between
carbon atoms forming a circle. In
contrast, aliphatic hydrocarbons lack
this delocalization.
Condensed structure of benzene
Benzene, toluene and xylenes
 are used extensively as raw materials for
the manufacture of drugs, plastics,
pesticides and other organic chemical
 It was discovered in 1970 that inhalation
of fumes of benzene lowered the white
blood corpuscles in humans and
caused leukemia in rats
FUSED- RING OR POLYNUCLEAR OR
POLYCYCLIC-AROMATIC HYDROCARBONS

 Benzene ring can fuse together to form

polycyclic aromatic hydrocarbons. The
simplest one is naphthalene ( C10H8).
 It is white crystalline substance used for
moth balls as moth repellant.

OTHER DERIVATIVES OF BENZENE

 Bromobenzeneis used as an additive to

motor oils, as a crystallizing solvent, and
in the production of the synthetic
intermediate phenyl magnesium
bromide
 Ethylbenzene is a naturally found in coal
tar and petroleum and is also found in
manufactured products such as inks,
pesticides, and
paints. Ethylbenzeneis used primarily to
make another chemical, styrene.
Other uses include as a solvent, in fuels,
and to make other chemicals.
 Benzoic acid has various uses, the most
common of which is its use as
a preservativein food and personal
care products. Because of its anti-
fungal properties, it's an ingredient
in topical anti-fungal cream, ointments,
and lotions that can help treat athlete's
foot and ringworm.
 Benzaldehydehas been classified as a
hazardous substance by the United
States Environmental Protection
Agency. Benzaldehyde is used as a
flavoring and fragrance in food,
cosmetics, pharmaceuticals, and soap
and is "generally regarded as safe" by
the US FDA.