NOTES - Unit 10: Organic Chemistry

PART 1: Functional Groups & Naming of Organic Compounds

Formulas for organic compounds: empirical, molecular and structural
Empirical: simplest whole number ratio of the atoms it contains.
Example: empirical formula of ethane, C2H6 is CH3
Molecular: actual number of atoms of each present. It can be deduced if both the empirical formula
and relative molecular mass, Mr, are known.
Example: What is the molecular formula of a compound with relative molecular mass, M r, of 30
and an empirical formula of CH3?

Structural: representation of molecule showing how the atoms are bonded to each other.
Full structural formula graphic formula showing every bond and atom. Usually 90 and 180
angles are used to show the bonds because this is the clearest representation on a 2-
dimensional page, although it is not the true geometry of the molecule. (MUST DRAW Hs!)
Condensed structural formula often omits bonds where they can be assumed, and groups
atoms together. It contains the minimum information needed to describe the molecule
unambiguously.
Stereochemical formula attempts to show the relative position of atoms and groups around
carbon in three dimensions. The convention is that a bond coming out of the page is shown as
a solid, enlarging wedge; a bond sticking behind the page is shown as a dotted line; a bond in
the plane of the paper is a solid line.
o Examples: methanol, CH3OH ethene, C2H4

Example: different formulas applied to three compounds

formula ethane ethanoic acid glucose
empirical

molecular

full structural

condensed
structural
IUPAC: International Union of Pure and Applied Chemistry
International, non-governmental organization that is best known for its system of nomenclature, which is now
recognized as the world authority in this field.

Rule #1: Identify the longest chain of carbon atoms

a) The longest chain of carbon atoms gives the stem/root of the name as shown in the table below:

# of C-atoms in longest chain Stem in IUPAC name Example (C2H2n+2 for alkanes)
1 meth- CH4, methane

2 eth- C2H6, ethane

3 prop- C3H8, propane

4 but- C4H10, butane

5 pent- C5H12, pentane

6 hex- C6H14, hexane

7 hept- C7H16, heptane

8 oct- C8H18, octane

9 non- C9H20, nonane

b) If two chains have equal lengths, pick the one with more branch points.

Rule #2: Number the carbons in the main chain

Number chain to minimize the position/number of the following in order of priority:
a) thing youre naming the compound after (double bond if alkene; -OH group if alcohol, etc)
note: for multiple double bonds -diene, -triene, -tetraene
b) first branch/substituent group
c) If both ends have the same first branching number, then number chain to minimize position of second
branch (and then third and so on).
d) if still in need of a tie breaker, minimize # of substituent group that comes first alphabetically

Note: in cyclic and aromatic (benzene derivatives) compounds, no number needed if only one substituent.

Rule #3: Identify the functional group and attach appropriate suffix
Note: the name for the stem/root is derived from the longest carbon chain, which may include the carbon of
the functional group.

Homologous Functional group Suffix in Example of compound

series IUPAC name
alkane -ane

alkene -ene

alkyne -yne

alcohol -anol

nitrile -anenitrile

aldehyde -anal

ketone -anone

carboxylic acid -anoic acid

ester* -anoate

amine* -anamine

amide* -anamide

*tricky naming described below:

Ester functional group*: organic salts where the alkyl group of the alcohol has replaced the hydrogen of the
carboxylic acid. Their name puts the alkyl group first, followed by the name of the acid anion.
Example: C2H5COOCH3

Amine functional group*: primary amines have an NH2 group which can undergo substitution by alkyl groups,
giving rise to secondary and tertiary amines. These are named using N- to show the position of the
substituents.
Example 1: (primary amine)
 Example 2: (secondary amine)

Example 3: (tertiary amine)

Amide functional group*: acid derivatives where the OH of the acid has been replaced by N<
Example 1: (primary amide)

Example 2: (secondary amide)

Example 3: (tertiary amide)

Indicating position of the functional group: shown by a number inserted before the functional group ending.
The number refers to the carbon atom to which the functional group is attached when the chain is numbered
starting at the end that will give the smallest number to the group.
Example 1: Example 2:

Sometimes a functional group can only be in one place, and in these cases we do not need to give a number to
show its position.
Example 1: Example 2:

Rule #4: Identify the side chains or substituent groups

Assign number of carbon at point of attachment.
Side chain/ Prefix in IUPAC Example of Compound
substituent name Condensed Structural formula name
group formula
 -CH3 methyl- CH3CH(CH3)CH3 2-methylpropane

-C2H5 ethyl CH(C2H5)3 3-ethylpentane

-C3H7 propyl- CH(C3H7)3 4-propylheptane

-F, -Cl, fluoro-, chloro-, CCl4 tetrachloromethane

-Br, -I bromo-, iodo-

-NH2 amino- CH2(NH2)COOH 2-aminoethanioic acid

Rule #5: Assemble name as a single word #, substituent, root, suffix

a) List substituents alphabetically (i.e. butyl- before methyl-)
b) If multiples of one substituent are present: di-, tri-, tetra, etc.
Note: di-, tri-, tetra, etc. arent part of alphabetical name (i.e. triethyl- before dimethyl-)
c) punctuation: commas between numbers; hyphens between numbers and letters; merged into one word
(exception: acid = word #2 for carboxylic acids)

EXAMPLES:
PART 2: Physical Properties & Isomerism (Structural- v. Stereo-)
Homologous series
Same general formula with neighboring members of the series differing by CH 2.

Examples:
Alkanes: CnH2n+2 Alcohols: CnH2n+1OH

Boiling points
Length of carbon chain

Structural isomers

Solubility in water
Determined by polarity

Example: ethanol v. 1-hexanol (or hexan-1-ol)

Classification of alcohols & halogenoalkanes

Alcohols and halogenoalkanes may be classified according to how many R- groups and how many hydrogen
atoms are bonded to the carbon atom containing the functional group.
Primary (one R-group Secondary (two R-groups Tertiary (three R-groups
bonded to C atom) bonded to C atom) bonded to C atom)
Unit 10: Organic Chemistry IB Topics 10 & 20 AP Chapters (Zumdahl): 21.4, 22(all) & beyond!
AP Chapters 1-5
Low reactivity of alkanes
C-C and C-H bonds
relatively strong
low polarity
Only readily undergo combustion rxns w/ O2 and substitution rxns with halogens in the presence of high energy UV light

Structural isomerism: same molecular formula, but different structural formulas

Ex: n-butane and 2-methylpropane

Ex: 1-butene, 2-butene and methylpropene

Structural isomers v. stereoisomers

Structural isomers: same molecular formula, but different structural formulas
Stereoisomers: same structural formula, but differ in their spatial arrangement
Geometrical isomerism
Optical isomerism

Stereoisomerism
1) Geometrical isomerism: occurs when rotation about a bond is restricted or prevented
Example: asymmetric non-cyclic alkenes
cis-2-butene v. trans-2-butene

Example: disubstituted cycloalkanes

cis- v. trans- form of 1,2-dichlorocyclopropane

Physical and chemical properties of geometrical isomers

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Different physical properties: (common)
cis-1,2-dichloroethene: b.p.=60.3C
trans-1,2-dichloroethene: b.p.=47.5C
Difference in both physical and chemical properties: (sometimes)
Ex: heating of cis- v. trans- forms of 2-butene-1,4-dioic acid

Stereoisomerism
2) Optical isomerism: shown by all compounds containing at least one asymmetric or chiral carbon atom within a
molecule (one that contains for different atoms or groups bonded to it).
o Two isomers are known as enantiomers and are mirror images of each other (like your right and left hand).
Example:

o Enantiomers are optically active with plane polarized light (both rotate plane-polarized light)
o Normal light consists of electromagnetic radiation vibrating in all planes when passed through a polarizing
filter the transmitted waves only vibrate in one plane and the light is said to be plane-polarized.

Enantiomers
o Apart from behavior toward plane-polarized light, enantiomers have identical physical properties.
o Chemical properties of enantiomers are also identical except when they interact with other optically active
substances.
o Often the case in the body, where different enantiomers can have completely different physiological
effects.
o Optical activity of enantiomers can be detected and measured by an instrument called a polarimeter.
o A polarimeter consists of a light source, two polarizing lenses, and between the lenses a tube to hold the sample
of the enantiomer.
o Diagram:

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o If the analyzer has to be rotated clockwise, the enantiomer is said to be dextrorotatory (from the Latin, dexter,
meaning right).
o If it has to be rotated counterclockwise, the enantiomer is said to be laevorotatory (from the Latin, laevus,
meaning left).
o One enantiomer is thus known as the d-form and the other is the l-form.
o If both enantiomers are present in equal amounts, the two rotations cancel each other out, and the mixture
appears to be optically inactive. Such a mixture is known as a racemic mixture.

Amino acid asparagine: H2N-CH(CH2CONH2)-COOH

One enantiomer tastes bitter
Other enantiomer tastes sweet

Enantiomers: Critical considerations: Thalidomide

One enantiomer combats morning sickness (labeled as sleep inducing above)

Other enantiomer responsible for fetal abnormalities (labeled as teratogenic above)
Drug released in 1958 by a German pharmaceutical company (sold OTC in some countries)
Reports of severe adverse side effects began to appear in 1959
Later is was found that clinical trials revealed these problems as early as 1956, yet the company released the drug anyway
Withdrawn from market in 1961
Has since been re-released (prescription only) to treat leprosy and certain types of cancer

PART 3: Reactions of Alkanes & Alkenes

Reactions of Alkanes
Combustion of alkanes
All hydrocarbons burn in excess oxygen to give carbon dioxide and water:
o CxHy + (x + y/4) O2 x CO2 + y/2 H2O
Although the C-C and C-H bonds (reactants) are strong, the C=O and O-H bonds (products) are stronger, so the
rxn is very exothermic.
o Ex: natural gas (methane)

o Ex: gasoline

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Unit 10: Organic Chemistry IB Topics 10 & 20 AP Chapters (Zumdahl): 21.4, 22(all) & beyond!
AP Chapters 1-5
Incomplete Combustion: If there is an insufficient supply of oxygen, incomplete combustion occurs and carbon monoxide
and carbon are also produced as products.

Substitution Reactions

Alkanes can react with halogens in the presence of UV light to form an acid and a substituted alkane.
o
Ex:

o
Ex:

Mechanism of chlorination of methane

The mechanism of an organic reaction describes the individual steps.

When a chemical bond breaks, it breaks heterolytically or homolytically.

Heterolytic fission: both of the shared electrons go to one atom, resulting in a negative and a positive ion.

Homolytic fission: each atoms keeps of the shared electrons, resulting in the formation of two free radicals.

The halogen-halogen bond is weaker than the C-H and C-C bond in methane and can break homolytically in the
presence of UV light.

This stage of the mechanism is called initiation:

Free radicals contain an unpaired electron and are highly reactive.

When a chlorine free radicals come into contact with a methane molecule they combine with a hydrogen atom
to produce hydrogen chloride and a methyl radical.

Since a new radical is produced, this stage of the mechanism is called propagation:

The methyl free radical is also extrememly reactive and reacts with a chlorine molecule to form the product and
regenerate another chlorine radical.

Another propagation step:

In theory a single chlorine radical may cause up to 10,000 molecules of chloromethane to be formed.

When two radicals react together, termination occurs:

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Further substitution can occur when chlorine radicals react with the substituted products.
o
For example:

The substitution can continue even further to produce trichloromethane and then tetrachloromethane.

The overall mechanism is called free radical substitution.
o
Note that in this mechanism hydrogen radicals, H, are not formed.

Reactions of Alkenes
Addition reactions

Bond enthalpies:
o
C-C 348 kJ mol-1
o
C=C 612 kJ mol-1 (less than twice C-C enthalpy)

Thus the C=C bond makes the molecule reactive.

The most important reactions of alkenes are addition reactions, where an unsaturated reactant becomes
saturated.

Addition reactions include the addition of hydrogen, bromine, hydrogen halides and water.

Uses of addition reactions
o
Bromination

Pure bromine is a red liquid, but has a yellow/orange color in soln.

When a soln of bromine is added to an alkene, the product is colorless.

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AP Chapters 1-5

Test for unsaturation: this decoloriation of bromine solution provides a useful test to indicate the
presence of an alkene group.
o
Hydration

Ethene is an important product formed during the cracking of oil.

Although ethanol can be made from the fermentation of starch and sugars, much industrial
ethanol is formed from the addition of steam to ethene.
o
Hydrogenation

The addition of hydrogen to unsaturated vegetable oils is used industrially to make margarine.

Hydrogenation reduces the number of double bonds in the polyunsaturated vegetable oils
present in the margarine, which causes it to become a solid at room temp (and have a longer
shelf life).

Addition polymerization

Under certain conditions, ethene can also undergo addition reactions with itself to form a long chain polymer
containing many thousands (typically 40,000 to 800,000) of carbon atoms.

These addition reaction scan be extended to other substituted alkenes to give a wide variety of different addition
polymers.
o
Example 1: formation of PVC

o
Example 2: formation of PTFE (Teflon)

PART 4: Reactions of Alcohols; Substitution Reactions

Reactions of Alcohols
Combustion

General eqn for an alcohol combusting completely in oxygen:
o
CnH(2n+1)OH(l) + (2n+1)O2(g) nCO2(g) + (n+1)H2O(l)

Ethanol is used as both a solvent and as a fuel. It combusts completely in excess oxygen to produce carbon
dioxide and water.
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C2H5OH(l) + 3O2(g) 2CO2(g) + 3H2O(l) H=-1371 kJmol-1

Ethanol is already partially oxidized, so it releases less energy than burning and alkane of comparable mass.

However, it can be obtained by the fermentation of biomass; thus, in some countries it is mixed with gasoline to
produce gasohol which decreases dependence on crude oil.
Oxidation of alcohols

Ethanol can be readily oxidized by warming with an acidified soln of potassium dichromate (VI). During the
process, the orange dichromate(VI) ion Cr2O72- is reduced from an oxidation state of +6 to the green Cr 3+ ion.

Breathalyzer test: blow into bag through tube of acidified KCr 2O7 crystals. If orange crystals turn green, this
indicates presence of a lot of ethanol (high BAC).

Ethanol is initially oxidized to ethanal. The ethanal is then oxidized further to ethanoic acid.

To stop rxn at ethanal stage, distill ethanal from the rxn mixture as soon as it is formed.

If complete oxidation to ethanoic acid is desired, heat the mixture under reflux so that none of the ethanal can
escape.

Ethanol is a primary alcohol. The oxidation reactions of alcohols can be used to distinguish between primary, secondary
and tertiary alcohols.

All primary (1) alcohols are oxidized by acidified KCr2O7, first to aldehydes then to carboxyllic acids.

All secondary (2) alcohols are oxidized to ketones, which cannot undergo further oxidation.

Tertiarary (3) alcohols cannot be oxidized by acidified K2Cr2O7 as they have no hydrogen atoms attached directly
to the carbon atom containing the OH group.

It is not true to say that tertiary alcohols can never be oxidized, as they burn readily. However, when this
happens, the carbon chain is destroyed.
Substitution reactions and reaction pathways
Substitution reactions of halogenoalkanes

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Because of the greater electronegativity of the halogen atom compared with the carbon atom, halogenoalkanes
have a polar bond.

Reagents that have a non-bonding pair of electrons are attracted to the carbon atom in halogenoalkanes and a
substitution rxn occurs.

Such reagents are called nucleophiles.

Mechanism of nucleophilic substitution

Primary halogenoalkanes (one alkyl group attached to the carbon atom bonded to the halogen)
o
Example: CH3CH2Br + OH- CH3CH2Br + Br-

Determined experimentally: rate=k[C 2H5Br][OH-]

The proposed mechanism involves the formation of a transition state which involves both of the
reactants.

Because the molecularity of this single-step mechanism is two it is known as an S N2 mechanism
(bimolecular nucleophilic substitution).
o
Primary halogenoalkanes tend to react by an SN2 mechanism.
(bimolecular nucleophilic substitution)

Tertiary halogenoalkanes (three alkyl groups attached to the carbon atom bonded to the halogen).
o
Example: C(CH3)3Br + OH- C(CH3)3OH + Br-

Determined experimentally: rate=k[C(CH3)3Br]

A two-step mechanism is proposed that is consistent with this rate expression.

The 1st step is rate-determining. Because the molecularity is one the mechanism is known as SN1
(unimolecular nucleophilic substitution).
o
Tertiary halogenoalkanes tend to react by an SN1 mechanism.
(unimolecular nucleophilic substitution)

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What about secondary halogenoalkanes?
o
Proceed by a mixture of SN1 and SN2 mechanisms

You need to be able to deduce rxn pathways given the starting material and the product.

Conversions with more than two stages will not be assessed.

Reagents, conditions and equations should be included.
Example: deduce a reaction pathway for the conversion of 2-butene to butanone can be done in two stages:

Step 1: 2-butene can be heated with steam and a catalyst to form 2-butanol.

Step 2: 2-butanol can then be oxidized by heating with acidified KCr 2O7 to form butanone.

PART 5: SN1&SN2; Elimination & Condensation Rxns

Nucleophilic Substitution

Common nucleophiles include OH- (from dilute NaOH soln), CN-, NH3 and H2O.

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+
The nucleophiles are attracted to the carbon atom and substitute the halogen atom in halogenoalkanes.

Primary halogenoalkanes react by an SN2 mechanism.

Tertiary halogenoalkanes react by an SN1 mechanism.

Factors affecting the rate of nucleophilic substitution

1) The nature of the nucleophile
o
Effectiveness of nucleophile depends on its electron density.

Anions tend to be more reactive than the corresponding neutral species.

Ex: the rate of substitution w/ OH- is faster than with H2O.

Among species with same charge, a less electronegative atom carrying a non-bonded pair of
electrons is a better nucleophile than a more electronegative one.

NH3 is a better nucleophile than H2O

This is because the less electronegative atom can more easily donate its pair of electrons
as they are held less strongly.

Example: Put the following nucleophiles on order of increasing reactivity: NH 3, H2O, CN-, OH-

2) The nature of the halogen

o
For both SN1 an SN2 rxns, iodoalkanes react faster than bromoalkanes, which react faster than
chloroalkanes.

C-I bond is weaker than the C-Cl bond and breaks more readily.
3) The nature of the halogenoalkane
o
Tertiary react faster than secondary, which are faster than primary halogenoalkanes.
o
The SN1 route is faster than the SN2 route

SN1 involves formation of intermediate carbocation

SN2 involves a transition state w/ relatively high activation energy

Substitution with ammonia and potassium cyanide

Halogenoalkanes can react with NH3 to form amines and with CN- to form nitriles.

With 1 halogenoalkanes the mechanism is SN2.
o
Example: bromoethane + CN-

o
Example: bromoethane + NH3

The rxn with KCN provides a means for extending the C-chain length by one C.

The nitrile can then be converted either into amines by reduction using H2 with a Ni catalyst or into carboxyllic
acid by acid hydrolysis.
o
Example:

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AP Chapters 1-5

Elimination and Condensation Reactions

Elimination rxns of halogenoalkanes

Altering rxn conditions can cause same reactants to make completely different products.
o
Example:

With dilute NaOH soln, the OH- ion acts as a nucleophile and substitution occurs to produce an
alcohol.

With hot alcoholic NaOH soln (i.e. NaOH dissolved in ethanol), elimination occurs and an alkene
is formed.

In this second rxn, OH- acts as a base. Elimination of HBr can proceed by either a
carbocation or as a concerted process

In the presence of ethanol there will also be some ethoxide ions present.

Ethoxide is a stronger base than OH-, so the equilibrium lies to the left but some
ethoxide ions will be present and these may be the actual species acting as the base.

Condensation rxns
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AP Chapters 1-5

Rxns between 2 molecules to form a larger molecule with the elimination of a small molecule such as H2O or
HCl.
o
alcohol + carboxylic acid ester + water

Example:

Esters

Most have distinctive, pleasant, fruity smell

Many uses:
o
Used as natural and artificial flavoring agents in food
o
Used as solvents in perfumes
o
used as plasticizers, substances used to modify the properties of polymers (i.e. PVC) by making them
more flexible.

Phthalate esters (esters of phthalic acid) - Many health concerns!
More condensation rxns
o
Example: Show the general rxn for a carboxylic acid with an amine.

This rxn is important in biological rxns --- amino acids contain an amine group and a carboxylic acid group , thus
amino acids can condense together in the presence of enzymes to form poly(amides).

Condensation polymerization

If each of the reactants in a condensation rxn contains two functional groups that can undergo condensation,
then the condensation can continue to form a polymer.
o
Example: benzene-1,4-dicarboxylic acid + ethane-1,2-diol

o
Example: hexane-1,6-dioic acid + 1,6-diaminohexane

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Example: Propose a process for the conversion of 1-bromopropane to 1-aminobutane (a.k.a. 1-butylamine)
o
Step 1:

o
Step 2:

Example: Propose a process for the conversion ethane into ethylamine
o
Step 1:

o
Step 2:

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