ORGANIC CHEMISTRY

Organic chemistry is the study of carbon-containing compounds. As carbon can bond to

itself stably 4 times, including double and triple bonds, forming both rings and
chains/branched chains, the possible number of compounds is virtually limitless. Living
things are composed primarily of carbon-containing compounds, and a diverse number
of products such as plastics, medicines, fuels, etc. are composed of hydrocarbons or
start with hydrocarbons. The major topics under study this unit are:
 Organic Nomenclature
 Types of Organic Reactions
 Reaction Mechanisms (advanced material)

HYDROCARBONS

A hydrocarbon is any compound that contains hydrogen and carbon. There are
significantly more organic compounds than inorganic compounds due to the bonding
properties of carbon. Carbon forms four strong covalent bonds, it can bond strongly to
itself (including ring, sheet, tube, and spherical structures), and it can form single,
double, and triple bonds. Hydrocarbons can generally be divided into three major
classes of molecules: 1) aliphatics, which include the alkanes, alkenes, and alkynes (and
which will be the focus of this course, 2) aromatics, which include one or more benzene
rings, and 3) hydrocarbon derivatives, such as alcohols, amines, esters, etc.

Organic nomenclature is the representation/identification of organic compounds using

formulas and names (you have previously been exposed to inorganic nomenclature in
Grade 10 and Unit 1 of this course). Instead of typical chemical formulas, organic
compounds are generally represented using what are called structural formulas, such as
an expanded molecular formula, which show the groupings of atoms (ex: CH3CH2CH3 as
opposed to C3H8), or line structures, which will be primarily used in this course.

Drawing Organic Line Structures

Line structures are generally used to represent the chemical formula of an organic
compound, while giving details about the structure of the compound. The advantage of
using line structures over other methods (such as a condensed formula) is that is gives
an indication of three-dimensional shape, and it is cleaner/easier/faster to draw and
read. In general, use the following rules:

1) a chemical bond is represented using a line

2) a carbon atom is represented as the endpoint of a line (assuming there are no other
atoms present, such as oxygen, nitrogen, etc.)
3) hydrogen atoms attached to carbons are assumed (remember: all carbons must have
four bonds)
4) all other atoms (N, O, F, etc.) are represented using their usual chemical symbols
5) single bonds are bent, single bonds branched off of double bonds are also bent, and
triple bonds are straight.

Examples:
 F OH

Organic Naming Rules (IUPAC)

The names of organic compounds often look quite confusing, but they are actually very
systematic. In fact, they all follow the general basic format:

PREFIX + ROOT + SUFFIX

Suffix:
1) indicates the functional group/type of compound (for compounds with more than one
functional group, the highest priority functional group is indicated. As a general rule, O >
N > halogens/alkyl groups).
2) when there is more than one of the same type of major functional group, use
modifiers such as “di”, “tri”, etc. immediately before the suffix (ex: diol), and use numbers
(again written immediately before the suffix) to locate the functional group(s)
(ex: 1,3-diol).

Root:
1) indicates the number of carbons (see Table 1- note the prefixes continue indefinitely)
in the longest continuous chain that contains the functional group. The chain must be
numbered so that the functional group(s) gets the lowest number- if there is a tie for
lowest number, break the tie alphabetically.

Table 1: Carbon numerical prefixes

Number of C 1 2 3 4 5 6 7 8 9 10 11 12
Name meth eth prop but pent hex hept oct non dec undec dodec
You should try to know up to C=19, as it is a very systematic pattern

Prefix:
1) all substituents not part of the main chain (root) are considered branches. The
branches need to be: i) located with a number- give branches the lowest possible
number(s), if there is a tie, break it alphabetically, and ii) identified with a name- use the
usual name for alkyl branches (see Table 1), but change the ending to “yl”. For
halogens, change the ending to “o”. Refer to Table 2 for branch names for other
functional groups. All branches must be organized alphabetically, with the numbers
written first, in ascending order, with the numbers separated by commas, and the
numbers separated from the words by dashes. If there are more than one of the same
type of branch, use the numerical prefixes (“di”, “tri”, etc.). The last branch is combined
with the root.
The above rules are good use as a general set of guidelines for any organic compound.
We will be looking at some specific, simple types of organic compounds that require us
to specify/modify some of the above guidelines.

ORGANIC FUNCTIONAL GROUPS

A functional group is the site of chemical reactivity in an organic molecule. The

functional group also determines the suffix of the molecule when naming, and is given
the highest priority (lowest number); when there are more than one functional groups in
a molecule, priority is given to the group with the largest molecular mass.

Alkanes
Alkanes are saturated hydrocarbons (all single bonds, all contain the maximum number
of hydrogen atoms possible). The suffix used is "ane", and the root is determined by
finding the longest continuous chain of carbons. Everything else in the molecule is
considered as a branch, and these branches are numbered so as to get the lowest
numbers (the lowest numbers does not necessarily mean the lowest sum of numbers).
All of the branches are organized alphabetically as the prefix. There are no functional
groups, therefore alkanes are not very reactive.

Alkenes
Alkenes contain one or more double bonds, and are therefore considered unsaturated
hydrocarbons. The suffix is "ene", and the root is determined by finding the longest
continuous chain of carbons that contains the double bond. The double bond must also
be located. Branches are determined as usual, except the double bond takes
precedence over any aliphatic (hydrocarbon) branches. Also, the double bond often
needs to be classified as either "cis" (Z) or "trans" (E), and this indicator(s) is written at
the very front of the prefix, in brackets. The reason that cis/trans identification is
necessary is because bonds attached to double bonds do not rotate, therefore their
positions are fixed in space. Even this subtle difference results in different physical and
chemical properties, thus a distinction must be made.

Example:

(2E)-but-2-ene (2Z)-but-2-ene

Alkynes
Alkynes contain one or more triple bonds (and are therefore unsaturated). The suffix is
"yne", and the multiple bond(s) must be located. All the same rules as per alkenes apply
for alkynes, except there are no cis/trans bonds for alkynes- this is because the bonds
off of the triple bond are linear. Note that in molecules with both double and triple bonds,
the double bond takes priority (as it is alphabetically lower, ene vs. yne). Alkynes are
more reactive than alkenes due to the presence of two pi (π) bonds.

Cyclics
Hydrocarbons, including, but not limited to, Alkanes, Alkenes, and to a limited extent,
Alkynes, can form cyclic or ring structures, where there is a least one fully enclosed loop
of carbons. In general, the number of carbon atoms in the ring structure defines the
root, and the prefix "cyclo" is used immediately in front of the root. In some instances,
such as when the branches off of the ring are especially complex, the ring is considered
as a "cyclo" branch(es).

Carboxylic acids
Contains a carbonyl group (a carbonyl group is a carbon double bonded to an oxygen)
attached to an alkyl group and a hydroxyl group. They are reactive due to the presence
of the electrophilic carbonyl group. The suffix is “oic acid”, and the branch name is
“carboxylic acid” O
R
OH

Esters
Contains a carbonyl group attached to an alkyl group and an oxygen atom bonded to
another alkyl group. Somewhat less reactive than a carboxylic acid. The suffix is “oate”,
and the branch name is “carboxamate”
O
R
O R

Amides
Contains a carbonyl group attached to an alkyl group and a nitrogen atom which can be
bonded to hydrogens and/or alkyl groups. Somewhat less reactive than a carboxylic
acid. The suffix is “amide”, and the branch name is “carboxamide”

O O
O
R R
R
N R NH R
NH2
R

Aldehydes
Contains a carbonyl group attached to an alkyl group and a terminal hydrogen atom.
Not very reactive due to the inability of the hydrogen atom to stabilize any intermediate.
The suffix is “al”, and the branch name is “carbaldehyde” O

R H
 Ketones
Contains a carbonyl group attached to an alkyl group on both sides of the carbonyl
carbon. Generally quite unreactive. The suffix is “one”, and the branch name is “oxo”

Nitriles R R
Contains a carbon atom triple-bonded to a nitrogen atom. Generally not very reactive.
The suffix is “nitrile”, and the branch name is “cyano”
R N

Alchohols
Contains a hydroxyl group. Quite reactive, and involved in several different types of
reactions. The suffix is “ol”, and the branch name is “hydroxy”
R OH

Amines
Contains at least one amino group. Generally non-reactive. The suffix is “amine”, and
the branch name is “amino”
R R
R NH2 R NH R N

Ethers
Contains an oxygen atom bonded to 2 alkyl groups. Generally non-reactive. There is no
suffix, rather ethers are named as branches, specifically “oxy” branches (ex: methoxy);
this is analogous to alkanes, and in a similar fashion, there essentially is no functional
group.
R O R
ISOMERS and STEREOISOMERS

ISOMERS

Isomers are compounds that have identical molecular formulas but differ in the ways in
which the atoms are bonded to each other. They come in two general forms: 1)
Constitutional isomers, which differ in the order and the way in which the atoms are
bonded together in their molecules, and 2) Stereoisomers, which have the same
connectivities but differ in the arrangement of their atoms in space. For both types, as
the number of atoms in a molecule increases, the number of possible structures
increases rapidly, and each isomer (constitutional and stereo) has different chemical
and/or physical properties.

Stereoisomers

There are two subsets of stereoisomers: 1) conformational, which are different

arrangements in space of the atoms within the molecule due to rotations around single
bonds, and 2) configurational, which differ from each other only in the arrangement of
their atoms in space and cannot be converted from one into another by rotations about
single bonds.

Conformational Isomers

Single bonds allow free rotation around their axes, resulting in different possible
conformations in space, and therefore different stereoisomers. Since all atoms have
electrons, and the electrons are negatively charged, and like charges repel, the
conformations where the atoms are further are apart are lower energy and thus
favoured. Newman projections are diagrams that show a view of a molecule down the
axis of a carbon-carbon bond, with the carbon atom toward the front represented by a
dot, and the own toward the rear by a circle. A select few Newman projections (for
ethane, butane, and cyclohexane) are shown below:

Figure 1: Newman projections for ethane, with the eclipsed conformation on the left, and
the lower energy staggered conformation on the right.
Figure 2: Newman projections for butane, with the highest energy eclipsed, gauche, then
another eclipsed, and the lowest energy staggered (or anti) conformations. Note that the
gauche conformation is lower in energy than eclipsed but higher in energy than
staggered.

Figure 3: Boat (left) and Chair (right) conformations of cyclohexane. The chair
conformation is more stable (lower energy) due to having two carbon atoms out of the
plane of the other four atoms. A similar situation arises with cyclopentane and its
envelope conformation being more stable, having one carbon out of the plane.

Configurational Isomers

In configurational isomers, the positions of the atoms are fixed in space and cannot
change due to rotations of bonds. A mirror image may be drawn of any molecular
structure. Stereoisomerism exists only when mirror images are not superimposable on
each other- these are called enantiomers. Enantiomers have identical physical
properties with one exception- they rotate plane-polarized light in opposite directions
(they are said to have optical activity). The electric vectors of a beam of unpolarized
light occur in all directions, but for plane polarized light the electric vectors travel only in
a single plane. It should be noted that a racemic mixture contains equal numbers of
molecules of two enantiomers and shows no optical rotation (as the two different
enantiomers effectively cancel each other out).

Figure 4: Enantiomers
Any object that cannot be superimposed on its mirror image is said to be chiral (it is
achiral if it is superimposable). An easy way to test for chirality is to look for a plane of
symmetry- if an object can be divided by a plane into two equal halves that are mirror
images of each other, the plane is a plane of symmetry, and the object/molecule is
achiral, and therefore not optically active. For molecules to be chiral, a starting
requirement is that there is a carbon atom (a central atom for simple cases) that is
bonded to four different substituents- this carbon is called a stereocenter.

Nomenclature of Stereoisomers:

The nomenclature rules for alkenes have been outlined previously (E, Z). These rules
focus on molecules with stereocenters, where a stereocenter is described as being R
(right-handed) or S (left-handed) and are called the Cahn-Ingold-Prelog rules:

1. Each group attached to the stereocenter is assigned a priority. The higher the atomic
number of the atom bonded directly to the stereocenter, the higher the priority of the
substituent.
2. If two identical atoms are attached to the stereocenter, the next atoms in both chains
are investigated until a difference is found. A priority assignment is made at the first
point at which atoms different priorities are found. A double bond is counted as two
single bonds, with the same principle for triple bonds (same concept applies to naming
organic compounds with more than one functional group or determing cis-trans
isomerism).
3. After priorities have been assigned, the molecule is viewed with the substituent of
lowest priority away from the viewer. If you can trace a clockwise path from group of
highest priority to the one of second priority and then to the one of third priority, the
stereocenter is assigned the R configuration. If the arrangement of the groups in order
of decreasing priority follows a counterclockwise path, the configuration is S.

Figure 5: (R)-2-hydroxypropanoic acid and (S)-2-hydroxypropanoic acid

PHYSICAL PROPERTIES – ORGANIC MOLECULES

A physical property is a descriptor of matter (ex: odour, colour, solubility, etc.). Physical
properties are predominantly determined by intermolecular forces. Intermolecular
forces, while important, are significantly weaker than intramolecular forces (chemical
bonds). There are several different intermolecular forces that are of relevance for
organic (covalently bonded) molecules:

1) hydrogen-bonding
o The strongest of the intermolecular forces
o Only occurs between atoms H, N, O, and F

2) dipole-dipole forces
o Relatively strong intermolecular force
o Occurs when there is a relatively large difference in electronegativity (a measure
of how much an atom wants shared electrons in a chemical bond), AND when
there is an asymmetry/non-zero vector sum of dipoles. In other words, occurs in
polar molecules, or at least polar portions of a molecule.

3) dispersion forces
o The weakest intermolecular force
o All molecules have dispersion forces
o Arise due to the natural movement of electrons, which results in temporary
development of partial positive and partial negative regions
o The more atoms present, the more electrons, the more dispersion forces (larger
molecules have more dispersion forces)

There are many different physical properties. For example, solubility, melting points,
and boiling points.

a) solubility- a general rule is "like dissolves like". For example, for an organic molecule
(generally non-polar) to dissolve in water (polar molecule), the organic molecule must
have structural similarities to water. Small alcohols will readily dissolve in water,
whereas large alkanes will not.

b) melting point- the larger the melting point, the stronger the intermolecular forces.
When the only consideration is dispersion forces, then generally, larger molecules
and/or molecules that can physically "pack together" (such as compact, spherical
molecules), will have larger melting points.

c) boiling point- the larger the boiling point, the stronger the intermolecular forces. When
the only consideration is dispersion forces, then generally, larger molecules and/or
molecules with long straight/unbranched chains, that can physically associate with each
other more readily, will have larger boiling points.
TYPES of ORGANIC REACTIONS

There are several different types of organic chemical reactions; the key to learning them
is to realize that: a) the reaction ALWAYS occurs at the functional group, b) single bonds
are very strong and stable, and therefore not reactive (will not be broken under normal
circumstances), and c) a specific type of organic reactant will ALWAYS produce a
different specific type of organic product (ex: an alcohol reacts and produces a
carboxylic acid). The following is a summary of the types of organic reactions that will
be studied this unit:

Combustion
Oxygen (O2) is always one of the reactants, and the products are carbon dioxide (CO2)
and water (H2O) assuming complete combustion/excess oxygen. If the reactant
contains nitrogen, nitrous oxides (NOx) will also be produced.
Example:
Alcohol + O2  CO2 + H2O + energy

Cracking
Large hydrocarbons (typically containing more than 8 carbons) are broken into smaller
pieces through the addition of heat/energy.
Example:

C11H24 C4H10 + C5H12 + C6H14 + C7H16

Catalyst
(275oC)

Substitution
Involves the replacement of one substituent on a compound (usually a hydrogen) with
another (usually a halogen); occurs via a nucleophilic substitution mechanism (SN1 or
SN2). Note that aromatics undergo substitution (via an electrophilic substitution
mechanism) as there are no double bonds actually present in the molecule, so they
cannot undergo addition reactions. Ultraviolet light (λ) is often necessary to facilitate the
reaction.
Example:

OH Br
+ H2 O
H Br + CH3 CH3
H3C H3C
Addition
The pi (π) part(s) of a multiple bond is broken, along with new sigma (σ) bonds forming
on either side of the former multiple bond. Note that Markovnikov’s rule must be
observed, which states that any added hydrogen will add to the carbon that already is
bonded to more hydrogens. Occurs via an electrophilic addition mechanism.
Example:

CH3 H CH3 H
H3C H HBr
H C C H H C C H
C C

H H Br H H Br

2o 1o
Major Product Minor Product

Elimination
Essentially the reverse process of an addition reaction, where sigma bonds are broken
and a new pi bond(s) is formed. Requires acid catalysis and heat (∆) to facilitate the
reaction. Occurs via en E1 or E2 mechanism.
Example:
Strong Acid, ∆
+

Oxidation
The products have more bonds to oxygen and/or less bonds to hydrogen after the
reaction occurs. Always requires the presence of an oxidizing agent ([O]).
Example:
Secondary Alcohols can be oxidised to ketones but no further
OH O
Oxidation
NO RXN
R C H C
R R
R
No H present on carbinol atom,
H present on carbinol atom,
can NOT be further oxidized
may be oxidized
Reduction
The products have less bonds to oxygen and/or more bonds to hydrogen after the
reaction occurs. Always requires the presence of a reducing agent ([H]).
Example:

O H
O Pt
H3C CH2 CH2 C H
C + H2
H3C CH2 CH2 H H
1o Alcohol
Aldehyde

O O H
Pt
C + H2 H3C CH2 C CH2 CH3
H3C CH2 CH2 CH3
H
Ketone
2o Alcohol
Condensation
Involves two organic reactants which combine/condense to produce one organic product
and a water molecule(s). Requires acid catalysis and heat.
Example:
O O
Strong Acid, ∆
R1 O H C R1 O C + H2O
HO R2 R2
Ester
Alcohol Carboxylic Acid

Hydrolysis
Essentially the reverse of a condensation reaction, where a water molecule(s) is added
to an organic reactant, and it splits (lyses) the reactant into two separate organic
molecules. Requires acid catalysis and heat.
Example:

O H2SO4, ∆
O
+ H H
O C + H2N R2
C R1 O H
R1 NH R2
 Addition Polymerization
The pi (π) part(s) of a multiple bond is broken, along with new sigma (σ) bonds forming
on either side of the former multiple bond. Note that polymers undergo addition via a
slightly different mechanism (there is still addition to both sides of the double bond,
resulting in single bonds) which allows for indefinite propagation. Example:

R R R R
∆, high pressure
C C
C C
R R n
n R R

Condensation Polymerization
Involves monomers with functional groups on both “ends”, which combine/condense to
produce an organic product and a water molecule(s). Requires acid catalysis and heat.
Note that since polymers undergo condensation on both sides of the reactant, the
reaction is propagated indefinitely.
Example:

O O H H O O
H H
H2SO4, ∆ + nH2O
O C R C O C R2 C
HO C R C OH + HO C R2 OH
H
n
H
H H

n
REACTION MECHANISMS

A mechanism is a detailed reaction pathway that shows how and why given reactants
form specific products. There are several different types of mechanisms, we will focus
on the following common ones: Unimolecular nucleophilic substitution (SN1),
Biomolecular nucleophilic substitution (SN2), elimination (E1, and E2), and free-radical
substitution. It should be noted that substitution and elimination reactions almost always
occur in competition with each other- factors such as the nature of the reagents and the
solvents used help determine which reaction will be the major one in a given case.

The general principle for the majority of mechanisms, is that electrons flow from regions
of higher electron density to regions of lower electron density. This electron
movement/flow is represented using curved or curly arrows from regions of high to low
electron density.

Nucleophilic substitution reactions:

These types of reactions involve electron flow from a nucleophile, which is a species that
"seeks a nucleus" to which to donate a pair of electrons, to an electrophile, which is a
species that "seeks electrons" as they have a positive/delta positive charge and have
room in their orbitals to accept a pair of electrons.

There are several structural factors that affect the nucleophilicity of a given species:
1) For nucleophilies of the same period in the periodic table, nucleophilicity
decreases with increasing electronegativity
2) Anions are more powerful nucleophiles than their uncharged conjugate acids
3) For anions from a given group in the periodic table, nucleophilicity increases
going down the group
Rates of nucleophilic substitution reactions are higher in polar solvents that cannot
undergo hydrogen bonding (ex: acetone), as the nucleophiles are freer to participate in
the reaction.

A leaving group is a stable species that can be detached from a molecule with its
bonding electrons during a displacement reaction. It is this species that is substituted in
the nucleophilic substitution reactions. The same factors that make a species a weak
base also make it a good leaving group.

SN2:
Two species undergo bonding changes in the transition state of a reaction, which is
initiated by the approach of a nucleophile. The molecularity, which is the number of
particles participating in an elementary step (which is simply a single step in a reaction
mechanism), is always two. If a nucleophile can approach the carbon atom (electrophilic
carbon) before the carbon-halogen bond breaks, then the alkyl halide will undergo an
SN2 reaction. Therefore primary alkyl halide, as well as some secondary alkyl halides
will undergo SN2 reactions.
In summary, the order of reactivity of alkyl halides in SN2 reactions is:
CH3 > primary > secondary > tertiary
Figure 1: An SN2 reaction, with sulfur acting as the nucleophile

SN1:
Only one species undergoes changes in bonding in the transition state for the rate-
determining step of a reaction. The SN1 reaction takes place in two steps: 1) the
ionization of a halide, and 2) the reaction of the resulting carbocation with a
nucleophile(s). The molecularity is always one. If the carbon atom bearing the leaving
group (generally a halogen) is a tertiary halide, then the nucleophile cannot get close
enough to the electrophilic carbon atom for bonding to start. Therefore tertiary halides,
and some secondary alkyl halides react via an SN1 reaction, provided the reaction
occurs in an ionizing solvent.
In summary, the order of reactivity of alkyl halides in SN1 reactions is:
Tertiary > secondary > primary > CH3
Figure:

Elimination Reactions

Figure 2: An SN1 reaction. The ionization of the halide is the slow step.

An elimination reaction results when a proton and a leaving group are removed from
adjacent carbon atoms (generally by a strong base, which is also a nucleophile), giving
rise to a π bond between two carbon atoms. Elimination reactions are promoted by
strong bases, as well as sterically hindered bases, and high temperatures, with tertiary
being more reactive than secondary being more reactive than primary alkyl halides.

E2:
Bimolecular elimination reactions (E2) occur by removal of a proton and simultaneous
loss of a leaving group. The reaction gives rise to a mixture of alkenes in which the
more highly substituted alkene is formed in the larger amount. The more highly
substituted alkene is defined as the one with fewer hydrogen atoms on the carbon
involved in the double bond. The more highly substituted an alkene is, the more stable it
is.
The three key requirements for an E2 reaction are:

 Strong base (defined as a substance that readily accepts a proton, H+)

 Moderate or better leaving group
 The hydrogen to be removed is bonded to the carbon which is directly
bonded to the electrophilic carbon (the one attached to the leaving group,
H-C-C-L)

Figure 3: An E2 reaction.

E1:
Unimolecular elimination reactions (E1) always accompany SN1 reactions, and result
from the formation of a cation (carbocation).
The three key requirements for an E1 reaction:

 Moderate or better leaving group (I- is an example of an excellent leaving

group)
 Stable carbocation (carbocations are inherently unstable, but if they can
be stabilized through high electron density in adjacent atoms of the
molecule, this is preferred)
 Polar solvent; the solvent helps to stabilize the positive charge of the
carbocation (ex: CH3OH)

Figure 4: An E1 reaction.

In summary, the order of reactivity for alkyl halides in elimination reactions is:
Tertiary > secondary > primary