Fundamentals of Organic
Chemistry
1 2 3 4 bonds
HONC
What is organic chemistry?
• study of carbon, the compounds it makes, and
the reactions it undergoes
• over 16 million carbon-containing compounds
are known
• because the C-C single bond (348 kJ/mol) and
the C-H bond (412 kJ/mol) are strong, carbon
compounds are stable
• carbon can form chains and rings
Empirical, molecular & structural formulas
2
• empirical formula
– simplest ratio of
atoms in a
molecule
• molecular formula
– actual numbers
of atoms in a
molecule
Empirical
Formula
Molecular
Formula
CH4
CH4
CH3
C2H6
CH2O
C6H12O6
CH2
C4H8
CH2
C8H16
structural formula
• unambiguously shows how the atoms are
bonded together
• can use condensed structural formulas
– bonds are omitted, repeated groups put
together, side chains put in brackets
• CH3CH2CH2CH2CH2CH3
–or even CH3(CH2)4CH3
• CH3CH(CH3) CH2CH3
condensed
skeletal formula
– every vertex or end represents a carbon
– hydrogens are implied
Isomers
• structural isomers: compounds with the same
molecular formula but different structure
(arrangement of atoms)
• different isomers have different chemical
properties and different physical properties
such as melting point and boiling point
Structural
Formulas
for C4H10O
Isomers
Alkanes
Structural formulas for the isomers of noncyclic alkanes up to C6
• hydrocarbon chains where all the bonds
between carbons are SINGLE bonds
• therefore the chain is said to be saturated with
hydrogen
• draw out and write the structural formulas for all
isomers that can be formed by:
– CH4 C2H6 C3H8 C4H10 C5H12 C6H14
Richard Thornley
2:54
Naming the isomers (IUPAC) of non-cyclic
alkanes up to C6
1. determine the longest carbon chain
–
–
1
2
3
4
5
6
use the prefix to denote the number carbons
ending is -ane
MethEthPropButPentHex-
Monkeys
Eat
Peeled
Bananas
Naming the isomers (IUPAC) of non-cyclic
alkanes up to C6
1. Richard Thornley 3:35
2. Determine the longest carbon chain
–
1
2
3
4
5
6
Use the prefix to denote the number carbons
MethEthPropButPentHex-
Monkeys
Eat
Peeled
Bananas
3. use the suffix “-ane” to indicate that the substance
is an alkane
4. number the carbons in the chain consecutively,
starting at the end closest to a substituent
(groups attached to the main chain)…”most
busy end”
5. name and number the location of each
substituent
– the name of the substituent will be written before the main
chain
– alkyl groups are the simplest substituents (yl ending)
•
•
•
•
CH3 is methyl
C2H5 is ethyl (CH3-CH2)
C3H7 is propyl
C4H9 is butyl
6. use prefixes di-, tri-, tetra-, to indicate when
there are multiple side chains of the same type
7. use commas to separate numbers and hyphens
to separate numbers or letters.
8. name the side chains in alphabetical order
• How about C5H12? The isomers are:
Pentane
2-methyl-butane 2,2-dimethyl propane
Nomenclature Practice
Name this compound
CH3
H3C1 2
Cl
3 4
5
CH3
9 carbons = nonane
6
7
8
H3C9
Step #1: For a branched hydrocarbon, the longest
continuous chain of carbon atoms gives the root name
for the hydrocarbon
Nomenclature Practice
Name this compound
CH3
H3C1 2
Cl
3 4
5
CH3
6
9 carbons = nonane
CH3 = methyl
7
8
chlorine = chloro
H3C9
Step #2: When alkane groups appear as substituents, they are named
by dropping the -ane and adding -yl.
Nomenclature Practice
Name this compound
CH3
H3C1 2
Cl
3 4
5
9 carbons = nonane
CH3
6
CH3 = methyl
7
chlorine = chloro
8
H3C9
1
9 NOT
9
1
Step #3: The positions of substituent groups are
specified by numbering the longest chain of carbon
atoms sequentially, starting at the end closest to the
branching.
Nomenclature Practice
Name this compound
CH3
H3C1 2
Cl
3 4
5
CH3
9 carbons = nonane
6
CH3 = methyl
7
8
chlorine = chloro
H3C9
2-chloro-3,6-dimethylnonane
Step #4: The location and name of each substituent are
followed by the root alkane name. The substituents are
listed in alphabetical order (irrespective of any prefix),
and the prefixes di-, tri-, etc. are used to indicate
multiple identical substituents.
Alkenes and Alkynes
Structural formulas for the isomers of straight
chains
• alkenes have a double bond between two or more of
the carbons (alkynes have a triple bond)
• the carbons are unsaturated, not as many hydrogens
because double bonds are present
Richard Thornley 10.1.7 (1:37)
Naming the isomers (IUPAC) of straight chain
alkenes or alkynes up to C6
1. suffix changes to “-ene” for alkenes and “yne” for alkynes
2. when there are 4 or more carbon atoms in a
chain, the location of the double/triple
bond is indicated by a number
3. begin counting the carbons closest to the
end with the double or triple bond
– numbering the location of the multiple
bonds takes precedence over the location
of any substituents
but-1-ene
but-2-ene
methyl propene
Naming Practice!!!
CH2
CH3 CH2 C
CH2 CH3
CH2 C
CH3
CH3
choose the correct ending
ene
CH2
CH3 CH2 C
CH2 CH3
CH2 C
CH3
CH3
determine the longest carbon chain with
the double bond
ene
CH2
CH3 CH2 C
CH2 CH3
CH2 C
CH3
CH3
assign numbers to each carbon
ene
CH2
CH2 CH3
1
CH3 CH2 C
2
5
CH2 C
3
4
6
CH3
CH3
assign numbers to each carbon
ene
CH2
CH2 CH3
1
CH3 CH2 C
2
5
CH2 C
3
4
6
CH3
CH3
attach prefix (according to # of carbons)
1-hexene
ene
CH2
ethyl
CH2 CH3
1
CH3 CH2 C
2
5
CH2 C
3
4
CH3
6
CH3
methyl
methyl
determine name for side chains
1-hexene
CH2
ethyl
CH2 CH3
1
CH3 CH2 C
2
5
CH2 C
3
4
CH3
6
CH3
methyl
methyl
attach name of branches alphabetically
2-ethyl-4-methyl-4-methyl-1-hexene
CH2
ethyl
CH2 CH3
1
CH3 CH2 C
2
5
CH2 C
3
4
CH3
6
CH3
methyl
methyl
group similar branches
2-ethyl-4-methyl-4-methyl-1-hexene
CH2
ethyl
CH2 CH3
1
CH3 CH2 C
2
5
CH2 C
3
4
CH3
6
CH3
methyl
methyl
group similar branches
2-ethyl - 4,4 - dimethyl hex-1-ene
Alkenes
Structural formulas for the isomers of the straight
chain alkenes up to C6
• alkenes have a double bond between two or
more of the carbons
– chains are unsaturated
• suffix changes to -ene
• when there are 4 or more carbon atoms in a
chain, the location of the double bond is
indicated by a number
• begin counting the carbons closest to the end
with the C=C bond
• draw the structural formulas for all isomers that
can be formed by each
– C2H4
– C3H6
Richard Thornley 10.1.7 (1:37)
– C4H8
These are only straight chain isomers.
– C5H10
– C6H12
pent – 1 – ene
pent – 2 – ene
Functional Groups
• a part of the molecule that stands out as an unusual
or unique part of the molecule
• add these somewhere on alkanes and alkenes
• the molecule often has certain characteristics based
on a functional group
• the entire class of compounds is often named
according to the functional group they contain
• “R” in a structural formula of a molecule just stands
for any other atoms other than the functional group
website on functional groups click here
carboxyl
- found in carboxylic acids
- part of amino acids
- putrid smelling
ester
- found in esters
- sweet smelling
carbonyl
- found in ketones
- sweet, minty, camphor smelling
hydroxyl
- found in alcohols
- sweet, camphor smelling
amino
- found in amines
- fishy smelling
- in amino acids
Smells
• humans can tell the difference between
10,000 different odors
• a more distant sense allowing us to detect
small concentrations of airborne substances
– must be a gas
• therefore cannot smell ionic compounds since they are
normally solids at room temperature
• molecules fit into certain receptors sites in the
human body as a result of their shape
– signals are then sent to the brain
• compounds that have similar smells have
similar structural formulas
• polar molecules may “stick” to receptor sites
better than non-polar
Amino Acids/Proteins
• the molecular subunits/building blocks of proteins
(the essential building blocks for living organisms)
• 20 different amino acids are used to synthesize
almost all the proteins in almost all living cells
• protein formation
– link is between carboxyl group on one a.a.
and the amino group on the other.
– water is formed and remaining N and C link
together called a peptide bond
Protein movie