Introduction to Organic Chemistry

INTRODUCTION TO ORGANIC CHEMISTRY
organic chemistry is the most important branch of chemistry - but of
course it would be nothing without the many other areas of chemistry -
in fact all branches of chemistry should not be viewed in isolation,
even though they may often be taught in isolation
organic chemistry is all around us, life is based on organic chemistry,
the clothes we wear, the drugs we take, the cars we drive and the fuel
that propels them, wood, paper, plastics and paints
organic chemistry is the study of compounds containing carbon
the ability of carbon to form as many as 4 strong bonds to many other
atoms, e.g., carbon, hydrogen, oxygen, nitrogen, halogens, sulphur,
phosphorus ensures a virtual infinite number of possible compounds
the constituent atoms and their exact combination determines the
chemical and physical properties of compounds and hence their
suitability for applications
the organic chemistry for this first semester will consist of the following
topics
general introduction - structure and bonding, examples of
organic compounds, nomenclature, examples of organic reactions,
an introduction to reaction mechanisms
Alkanes - physical properties, synthesis, chemical properties
Alkenes - physical properties, synthesis, chemical properties
Alkynes - physical properties, synthesis, chemical properties
all examined as part of module 06510
recommended texts
Organic Chemistry by Solomons and Fryhle (8th edition) 2004
Organic Chemistry by Maitland Jones (3rd edition) 2004
Organic Chemistry by Clayden, Greeves, Warren, Wothers 2001

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TYPICAL ORGANIC COMPOUNDS
STRUCTURES AND NOMENCLATURE
hydrocarbons - contain carbon and hydrogen only
alkanes - fully saturated, all single bonds, chain and cyclic
there are many different ways to draw chemical structures, often it does
not matter which is used, but sometimes a full structure will be required
if reaction mechanisms are being considered, for example
the nomenclature of organic compounds follows the IUPAC system -
International Union of Pure and Applied Chemistry
first important IUPAC rule - names are based on the number of
carbon atoms present in the longest possible chain
H
H H
H
H
H
H C
H H C C H
H C C
C
H
H
H H
H
H
H
butane
methane
ethane
propane
CH3CH2CH2CH2CH3 CH3(CH2)4CH3
pentane
hexane
hept, oct, non, dec, undec, dodec,
what about branched chain systems?
take the longest chain - C5 - hence pentane,
number the chain so that the substituents have
the lowest possible numbers - hence
2,3-dimethylpentane
not 3,4-
note the commas and hyphens - very important
look carefully, you might think a pentane? but no
the longest chain is six - hence hexane - what is the
substituent? ethyl, at the 3- position - hence
3-ethylhexane
not 3-propylpentane!!!
same rules as above, then list substituents
alphabetically (ignore prefixes such as di and
tri; i.e., dimethyl comes after ethyl) - hence
4-ethyl-2-methylhexane
H3C
C2H5
same rules
for cyclics
Cl
1-ethyl-3-methylcyclohexane
4-chloro-2-ethyl-1-methylcyclohexane

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hydrocarbon sub-units with trivial names retained by IUPAC
H3C CH
trivial names persist in many cases beacuse they
are convenient, but often difficult to deal with - in
CH3
some cases the trivial names are common and
1-methylethyl or
have been retained under the IUPAC system
isopropyl
CH3
H
CH
3C
2
CH
H3C CH CH2
H3C C
CH3
CH3
CH3
1-methylpropyl or
2-methylpropyl or
1,1-dimethylethyl or
sec-butyl
isobutyl
tert-butyl
CH3
H
this is the only five-carbon unit with a
3C
C
CH2
trivial name allowed by IUPAC
CH3
2,2-dimethylpropyl or
neopentyl
the hydrogen atoms of an alkane are classified according to their
position - primary (1°), secondary (2°), tertiary (3°)
3° hydrogen atom
2° hydrogen atoms
H3C CH CH2 CH3
as we shall see later, the 'removal'
of a hydrogen atom leaves a
CH3
sub-unit that is classified 1°, 2° or 3°
as appropriate - of great significance
in organic reactions
1° hydrogen atoms
other common sub-units
X CH2
H
X
H
CH2 X
X
H
CH2
H
H
H
H
vinyl
allyl
benzyl
propargyl
the above sub-units are also of significance in organic reactions

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alkenes - unsaturated, C=C double bond, chain and cyclic
the nomenclature of alkenes follows the IUPAC system and is very
similar to that of alkanes - really very easy with experience
H
H
H
CH
H
CH
3
2CH3
note the same
prefix as for
H
H
H
H
H
H
alkanes
propene
but-1-ene
ethene
1-butene (USA)
note from butene we get
possible isomers, but-1-ene
and but-2-ene, and because
the π-bond restricts rotation
but-1-ene
trans-but-2-ene cis-but-2-ene
there are two isomers of
but-2-ene (cis and trans)
CH3CH=CHCH2CH2CH3
definitely trans
general formula,
obvious why
cis or trans not defined
trans-hex-2-ene
not trans-hex-4-ene
lowest possible number for double bond is chosen
note that the numbering is usually based on the position of the
double bond - not substituents, hence
H CH
H
3
trans-5,5-dimethylhex-2-ene
C C CH3
H
not trans-2,2-dimethylhex-4-ene
3C
H CH3
H
but not for alcohols!!!, which we have not even mentioned yet,
perhaps you know what they are!!!
OH
HO
4-methylpent-3-en-2-ol
2-methylcyclohex-2-en-1-ol
not 2-methylpent-2-en-4-ol
not 2-methylcyclohex-1-en-3-ol
speaking of cyclics!
very similar to acyclic alkenes,
but where the numbering is set
by the double bond at position 1
there is no need to include it
cyclohexene
3-methylcyclohexene

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alkynes - unsaturated, C≡C triple bond, chain and cyclic (rare)
the nomenclature of alkynes follows the IUPAC system and is very
similar to that of alkanes and alkenes - really very easy with experience
H C C H
CH
C C H
3
CH
C C CH
3
2CH2CH3
ethyne
propyne
hex-2-yne
not hex-4-yne
H C C CH
as for alkenes, with alcohols the OH takes
2CH2OH
preference for the numbering
but-3-yn-1-ol
H
H a double bond takes preference
over a triple bond for numbering
H
H H
pent-1-en-4-yne
H
not pent-4-en-1-yne
rules on branching just the same as for alkenes
aromatic systems - benzene rings
benzene is a simple aromatic system and extremely common, naming is
very easy!
most substituted benzenes are named easily as
a benzene derivative - but some are not!!
benzene
Br
OH
NO2
CH
CN
3
bromobenzene
toluene
ethylbenzene benzonitrile
phenol
nitrobenzenenot methylbenzene
not cyanobenzene
not hydroxybenzene
NO2
substituents are listed alphabetically -
as seen for other systems
Br
1-bromo-3-nitrobenzene
CN
OH
some suffixes have higher priorities than others
which forces the lower one to become a prefix
2-hydroxybenzonitrile
not 2-cyanophenol

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Representative Organic Compounds
haloalkanes or alkyl halides
Cl
I
Cl
Br
2-iodobutane
2-chloro-3-methylbutane (2-chloroethyl)benzene
benzyl
2°
2°
1°
bromide
1° - but a
note the primary (1°), secondary (2°), tertiary (3°)
bit special
designations, they give rise to different chemical reactivity
aryl halides
chemically, aryl halides are much
Cl
Br
less reactive than alkyl halides
chlorobenzene 2-bromonaphthalene
alcohols
OH
OH
OH
CH3CH2OH
ethanol
2-methylbutan-2-ol
cyclohexanol
benzyl alcohol
1°
3°
2°
1° - but a
bit special
phenols
the aromatic analogues of alcohols,
OH
but their chemical properties are
often different to those of alcohols
phenol
amines
NH2
H
Et
2N
Et
Et
propylamine
NH2
N
1°
isopropylamine
triethylamine
2-amino-2-methylbutane
1° not 2°
3°
1° not 3°
H
N
notice the way 1°, 2° and 3° amines
N
are made up, and how they differ
H
from 1°, 2° and 3° alcohols and
diisopropylamine
pyrrolidine
alkyl halides for example
2°
2°
ethers
O
O
O
ethoxyethane
2-methoxy-2-methylpropane
(ether)
tetrahydrofuran
(MTBE)
(THF)

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Representative Organic Compounds
aldehydes and ketones (carbonyl compounds)
essentially the same class of compound but given different names!!
O
O
O
O
H
H
H
methanal
propanone
pentanal
hexan-2-one
(acetone)
O
notice the difference between aldehydes and ketones -
a bit like primary and secondary
cyclohexanone
carboxylic acids and their derivatives
combine the carbonyl group of aldehydes and ketones with another
group on the same carbon - the other group can be hydroxyl (acids),
chloro (acid chlorides), acetyl (acid anhydrides), ether (esters),
amino (amides) - examples are shown below
O
O
O
O
O
O
H
O
Cl
O(CH
O
2)3CH3
NH2
ethanoic acid
ethanoyl chloride
ethanoic anhydride
butyl ethanoate
ethanamide
(acetic acid)
(acetyl chloride)
(acetic anhydride)
(butyl acetate)
(acetamide)
1° amide
O
O H
O
O
N Me
O
benzoic acid
Me
phenyl cyclohexanecarboxylate
N,N-dimethylbenzamide
3° amide
OEt
O
Ph
N
O
O
Et
H
ethyl benzoate
O
N-phenylethanamide
ethyl acetate
2° amide
(ethyl ethanoate)
nitriles (cyanides)
H3C
C
N
C N
C N
ethanenitrile
benzenecarbonitrile
cyclohexanecarbonitrile
(acetonitrile)
(benzonitrile)

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Orbital Hybridisation - models for bonding in organic compounds
Carbons in methane, ethane, cyclohexane for example
methane has the formula CH4, but what does this tell us about the
structure? - not much is the answer, but you may know that the
carbon atom is at the centre of a tetrahedron
experimental evidence shows methane and other analogues to have a
tetrahedral arrangement of atoms - all four bonds are equivalent with
each hydrogen as far from the next as possible - tetrahedral
how do we account for the tetrahedral shape given the ground state
electron configuration of carbon?
2p
2p
2sp3
2s
2s
1s
1s
1s
ground state
excited state
hybridised state
the ground state configuration would seemingly only give two bonds!
the excited state does allow four bonds, but not all would be equivalent!
but if the three 2p orbitals are hybridised with the 2s orbital then four new,
equivalent orbitals (2sp3) are generated which arrange as far apart as
possible (minimum energy) in a tetrahedral arrangement which allows
the formation of four equivalent bonds with angles of 109.5°
the bonds are called sigma bonds
if all four 2sp3 atomic orbitals overlap with 1s atomic orbitals of
hydrogen atoms, then methane is formed
if one 2sp3 atomic orbital overlaps with one from another carbon atom
and the remaining six overlap with 1s atomic orbitals of hydrogen atoms,
then ethane is formed - other combinations are obvious
it is appropriate at this point to look at atomic orbitals and molecular
orbitals, how they are defined and what shapes they are
note that this concept is only a model - orbitals and hybridisation
should not be considered real! - but the model does provide an
excellent explanation for reality!

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Atomic Orbitals
ψ2 represents the probability of finding an electron at a certain location
plots of ψ2 generate the shapes of atomic orbitals such as s, p, d and f
hence atomic orbitals result from quantum mechanics and represent
a region of space where the probability of finding an electron is large
electrons have the property of waves and can be positive and negative
or zero in value - the positives and negatives as shown in orbitals does
not indicate charge! and does not indicate a greater or a lesser
probability of finding an electron
examples of atomic orbitals
both the 1s and the 2s orbitals are spherical and the 2s orbital has a nodal
surface where ψ2 = 0 and the inner portion is negative
the 2p orbitals are dumb-bell shaped with two almost-touching spheres,
one is positive and one is negative, ψ2 = 0 at the nodal plane
nodal plane
(–)
(–)
(+)
(+)
(–)
(+)
2sp2 and 2sp
nodal
are similar
surface
2s
2p
2sp3
4
+
1s
109.5°
4x2sp3
methane
when two atomic orbitals combine they do so to produce two molecular
orbitals - combination with like signs (constructive) produces a bonding
molecular orbital, which is larger and so ψ2 is larger - combination with
opposite signs (destructive) produces an antibonding molecular orbital,
which is small, so ψ2 is small, and there is a nodal plane where ψ2 = 0

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Orbital Hybridisation - models for bonding in organic compounds
Carbons with C=C, C=O, C=N for example
we have just seen how we can account for the structure of alkanes
through hybridisation, but how do we account for the structure of
alkenes, carbonyls and imines for example
experimental evidence shows that these compounds at the bonding in
question are planar, so how do we account for this given the ground
state electron configuration of carbon?
2p
2p
2sp2
2s
2s
1s
1s
1s
ground state
excited state
hybridised state
the ground state configuration would seemingly only give two bonds!
the excited state does allow four bonds, but not to the required shape
a similar hybridisation 'occurs' to that seen for alkanes, but one of the
2p orbitals is left out and only two hybridise with the 2s orbital to give
three 2sp2 orbitals
the three 2sp2 orbitals arrange in a trigonal planar manner (maximum
distance apart, minimum energy) with angles of 120° between - like
those found in methane, these bonds are called sigma bonds
the remaining 2p orbital is perpendicular to the planar framework, and
overlaps with another p orbital, from one of the three attached units,
to form a pi (π) bond - hence creating a double bond
p orbital
sp2 orbital
two sp2
4
hybridised
1s
carbons
120° planar
ethene

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