MF111 Study Guide 6
Fundamental organic chemistry
Learning outcomes

Draw bond-line drawings of larger molecules

Identify functional groups within a complex molecule

Name small organic compounds according to the IUPAC system

Understand how nucleophiles and electrophiles participate in organic reactions

Recognize addition, substitution, elimination, oxidation and reduction reactions

Predict the products of addition, substitution, elimination, oxidation and reduction
reactions
Overview
Organic chemistry is a sub-discipline within chemistry involving the study of the structure,
properties, composition and reactions of carbon-based compounds. Organic compounds are
derived from hydrocarbons and may contain other elements such as nitrogen, oxygen,
phosphorus, sulphur and less commonly, halogens and silicon. They are structurally diverse and
form the basis of all life on earth. Because of their structural diversity, organic compounds have
a wide range of applications. These applications include plastics, drugs, petrochemicals, food,
explosive material, and paints.
Hydrocarbons
Carbon is a small atom in period 2 of Group 4A(14) in the periodic table. Like all Group 4A(14)
elements, carbon has 4 electrons in its valence shell and moderately high electronegativity (EN
2.5).
In most cases, carbon forms covalent compounds. Hydrocarbons are organic compounds
consisting entirely of hydrogen and carbon. As they comprise entirely of C−H bonds, they are
relatively non-polar (∆EN 0.4).
Major classes of hydrocarbons are listed in Figure 6.1. Most hydrocarbons are commercially
derived from petroleum for use as fuel, solvents and synthesis of more complicated organic
compounds such as plastics. However, because petroleum is a finite resource, finding renewable
alternatives is an area of current research. Palm oil for the production of biodiesel and
oleochemicals is being explored by many Malaysian oil palm companies.
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Figure 6.1 Major classes of hydrocarbons
Line drawings
Retinol is the most common form of vitamin A. Figure 6.2 is a straight-line drawing or
Kekulé structure that show how all atoms are bonded together (Similar to Lewis structure in
Study Guide 3). However, straight line drawings are only viable for small molecules. For
larger molecules such as retinol, showing all of the hydrogen atoms makes it difficult to
compare the overall structure with other similar molecules. It also makes it difficult to focus
in on the double bonds and OH group.
Question: How many OH groups are there in the drawing below?
Figure 6.2 Straight line drawing of retinol
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Figure 6.3 is a bond-line drawing for retinol that is much easier to draw than straight-line
drawings. Carbon atoms are represented as the vertices (sharp angles) and only bonds are shown.
Heteroatoms i.e. atoms that are not carbon are also shown. With this simplified representation, it
is also much easier to distinguish the single bonds, double bonds, OH group, CH3 groups and the
main ring and chain. You will learn to appreciate this type of formula writing after drawing a
countless number of organic molecules.
Figure 6.3 Bond-line drawing of retinol
Functional Groups
Functional groups are structural units within organic compounds that are defined by specific
bonding arrangements between specific atoms. It is important to be able to quickly recognize
common functional groups because of their unique chemical properties.
Halogen based groups
Alkanes bonded to a halogen are referred to as a haloalkane e.g. fluoroalkane, chloroalkane.
Dichloromethane, CH2Cl2, is an example of a haloalkane (Figure 6.4).
Figure 6.4 Dichloromethane, a haloalkane
commonly used as a solvent
Oxygen and sulphur based groups
Alcohols comprise a carbon is bonded to a hydroxyl group i.e. OH group. If the central carbon
in an alcohol is bonded to only one other carbon, we call the group a primary alcohol (Figure
6.5). In secondary alcohols and tertiary alcohols, the central carbon is bonded to two and three
carbons, respectively. Methanol (central atom not bonded to carbon) is in class by itself in this
respect.
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Figure 6.5 Primary, secondary and tertiary alcohols. Methanol belongs in a class of its own.
The sulphur analog of an alcohol is called a thiol, the prefix thio is Greek for sulphur (Figure
6.6).
Figure 6.6 Primary, secondary and tertiary thiols
Phenols comprise a hydroxyl group bonded to a benzene ring (Figure 6.7). They are
distinguished from alcohols because the H atom of the hydroxyl group ionises more readily. The
acidity of the hydroxyl group in phenols is commonly intermediate between that of aliphatic
alcohols and carboxylic acids (pKa ≈ 10 to 12).
Figure 6.7 Phenol, the simplest phenolic compound
Ethers comprise oxygen bonded to two carbons. Figure 6.8 shows the straight-line and bond-line
drawings of diethyl ether, a common laboratory solvent and one of the earliest medical
anaesthetics.
Figure 6.8 Straight-line and bond-line drawings of diethyl ether
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Sulphides, are the sulphur analog of ether (Figure 6.9).
Figure 6.9 Diethyl sulphide and thiane (heterocyclic sulphide)
Ketones and aldehydes are two closely related carbonyl-based functional groups (C=O) that
react in very similar ways (Figure 6.10). In a ketone, the carbon atom of a carbonyl is bonded to
two other carbons. In an aldehyde, the carbonyl carbon is bonded on one side to a hydrogen, and
on the other side to a carbon.
Figure 6.10 Aldehydes (formaldehyde and acetaldehyde) and a ketone (acetone).
Nitrogen based groups
Amines comprise nitrogen bonded to carbon. Amines are classified as primary, secondary, and
tertiary amines based on the number of carbons the nitrogen is bonded to (Figure 6.11). Amines
behave like ammonia in that its lone pair can form a coordinate bond with water to yield an OH −
ion. However, ammonia is usually not considered an organic compound (no carbon).
Figure 6.11 Primary, secondary and tertiary amines alongside ammonia.
Imines and nitriles are molecules with carbon-nitrogen double bonds and triple bonds,
respectively. (Figure 6.12). Nitriles are also often referred to as cyano groups.
Figure 6.12 An imine and a nitrile
Phosphorus based groups
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Phosphate groups are esters of phosphoric acids (Figure 6.8). Many biological molecules
contain phosphate, diphosphate (also called pyrophosphate), and triphosphate groups.
Figure 6.13 Inorganic phosphate, organic monophosphate and organic diphosphate
Because phosphates are so abundant in biological organic chemistry, it is convenient to depict
them with the abbreviation 'P' (Figure 6.9). Notice that this 'P' abbreviation includes the oxygen
atoms and negative charges associated with the phosphate groups.
Figure 6.14 Abbreviated forms of monophosphate and pyrophospate esters
Carboxylic acid derivatives
Carboxylic acids and their derivatives has been separated from the other oxygen based groups
because of their diversity. A carboxyl or carboxylic acid group comprises a carbonyl carbon
bonded to a hydroxyl group (Figure 6.15).
Figure 6.15 Simple carboxylic acids, formic acid and acetic acid
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As the name implies, carboxylic acids are acidic, and their hydroxyl hydrogen readily ionises
(pKa ≈ 1 to 5). Deprotonation results in a conjugate base called a called a carboxylate ion
(Figure 6.16).
Figure 6.16 Conjugate bases of formic acid and acetic acid
Carboxylic acid derivatives are a group of compounds that contains a carbonyl group but the
OH group is replaced by an electronegative atom, usually oxygen, nitrogen, or a halogen.
In esters, the carbonyl carbon is bonded to an oxygen which is itself bonded to another
carbon. Another way of thinking of an ester is that it is a carbonyl bonded to an alcohol (Figure
6.17). Thioesters are similar to esters, except a sulfur is in place of the oxygen.
Figure 6.17 Ester and thioester functional groups
An acid chloride comprises a carbonyl carbon is bonded to a chlorine (Figure 6.18).
Figure 6.18 An acid chloride
In amides, the carbonyl carbon is bonded to a nitrogen. The nitrogen in an amide can be bonded
either to hydrogens, to carbons, or to both. Another way of thinking of an amide is that it is a
carbonyl bonded to an amine.
Figure 6.19 Different examples of amides
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Multiple functional groups
A single compound often contains several functional groups. This is especially true for large
molecules such as (+)-Vinblastine, an anticancer drug. Question What are the six types of
functional groups present in (+)-Vinblastine?
Naming organic compounds
Naming of organic molecules usually follows a system has been devised by the International
Union of Pure and Applied Chemistry (IUPAC). The IUPAC system is convenient for naming
relatively small, simple organic compounds.
Alkanes are named with the suffix –ane and the prefix is determined by the number of carbons
(Table 6.1). Alkene and Alkynes follow a similar naming convention followed by the suffix –ene
and –yne, respectively.
Table 6.1 Prefixes for naming organic compounds
Carbon
Prefix
1
Met–
2
Eth–
3
Prop–
4
But–
5
Pent–
6
Hex–
7
Hept–
8
Oct–
9
Non–
10
Dec–
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Other functional groups are named with different suffixes as shown in Table 6.3.
Table 6.2 Common suffixes for naming organic compounds
Functional
suffix
group
Alkane
–ane
Alkene
–ene
Alkyne
–yne
Alcohol
–ol
Thiol
–thiol
Aldehyde
–al
Ketone
–one
Carboxyl
–oic (acid)
–oate (conjugate base)
Acid chloride
–oyl chloride
Amine
–amine
Amide
–amide
Imine
–imine
Question: How would you name palmitic acid, an unsaturated fatty acid with 16 carbons?
In larger molecules, it becomes important to assign a number to indicate the position of
functional groups. Functional groups are assigned the smallest possible number as shown in the
example below involving a chloroalkane (Figure 6.20).
Figure 6.20 Numbering of functional groups
Functional groups that have characteristic suffixes such as those in Table 6.2 can also be
numbered to indicate their position (Figure 6.21).
Figure 6.21 Numbering of functional groups with characteristic suffixes
If the molecule has multiple branches, the main ‘parent’ chain with the most carbons has to be
identified. Hydrocarbon chains that are not part of the main parent chain are refer to as alkyl
groups named according to their length e.g. methyl, ethyl, and propyl (Figure 6.22).
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Figure 6.22 Numbering of hydrocarbons with multiple chains
Notice in Figure 6.23, the ‘ethyl group’ is not treated as a substituent, rather it is included as part
of the parent chain, and instead the methyl group is treated as a substituent. The IUPAC name
for straight-chain hydrocarbons is always based in the longest possible parent chain.
Figure 6.23 Correct identification of parent chain
Cyclic structures are assigned the prefix cyclo− (Figure 6.24).
Figure 6.24 Cyclic hydrocarbons
In the case of multiple substituents, the prefixes di, tri, and tetra are used (Figure 6.25). Again
each subsistent is assigned the smallest possible number.
Figure 6.25 Molecules with multiple substituents
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Ethers and sulphides are designated by naming the two groups on either side of the oxygen or
sulphur (Figure 6.26).
Figure 6.26 Naming ethers and sulphides
For esters, the group attached to the oxygen (alcohol group) is named first, followed by the name
of the remaining carboxylate group.
Figure 6.27 Naming esters
If an amide has an unsubstituted –NH2 group, the suffix is simply ‘amide’. In the case of a
substituted amide, the group attached to the amide nitrogen is named first, along with the letter
‘N’ to clarify where this group is located. Secondary and tertiary amines are also named using a
similar nomenclature.
Figure 6.25 Naming substituted and unsubstituted amides
There are many more rules in the IUPAC system. The IUPAC naming of larger molecules with
multiple functional groups and substituents can get very unpractical. However, IUPAC
sometimes publishes special rules for numbering large biomolecules like flavonoids. Figure 6.26
shows a flavonoid with antioxidant and anticancer properties, and a very long IUPAC name:
3,3’,4’,5,7-Pentahydroxyflavone 3-β-glucoside. Because of the long IUPAC name, it is more
convenient to call it by its non-IUPAC name: quercetin-3-glucoside. The “3” indicates that
glucose is attached to the 3 carbon of quercetin.
Figure 6.26
Quercetin-3-glucoside
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Organic reactions
Most organic reactions occur via of the interactions of nucleophiles and electrophiles (Figure
6.27).
A nucleophile is an atom that donates an electron-pair to an electrophile to form a chemical
bond in a reaction. All atoms or ions with a free pair of electrons or at least one double bond can
act as nucleophiles. Because nucleophiles donate electrons, they are by definition Lewis bases.
An electrophile is an atom that is attracted to electrons and participates in a chemical reaction by
accepting an electron pair in order to bond to a nucleophile. Because electrophiles accept
electrons, they are Lewis acids. Most (but not all) electrophiles are positively charged or have an
atom that carries a partial positive charge.
Figure 6.27 Nucleophile (B) donating its electron pair to electrophile (A)
Addition reactions
Addition reactions occur when an atom or group of atoms is added to a molecule without the loss
of any other atom or group of atoms.
Alkene
Alkenes readily undergo addition reactions with halogens. Figure 6.28 shows a reaction between
bromine liquid and an alkene to form a dibromoalkane. A similar reaction that requires nickel as
a catalyst is used to add hydrogen to unsaturated oils for the manufacture of margarine.
Figure 6.28 Addition reaction between ethane and bromine
Alkenes also readily undergo addition reactions with hydrogen halides. However, in the case of
asymmetric alkenes, the reaction can result in two possible products (Figure 6.29). In such cases,
the Markovnikov Rule applies, favouring the addition of the acidic hydrogen to the carbon that
has the greater number of hydrogen atoms already attached to it.
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Figure 6.29 Addition of HCl to propene, an asymmetric alkene. The reaction almost exclusively
favours the formation of 2-chloropropane (B).
Question: Would addition of HCl to 2-pentene favour 2-chloropentane or 3-chloropentane?
Carbonyl
Carbonyl groups readily undergo a reversible addition reaction with water to form carbonyl
hydrates. Carbonyl compounds are often in equilibrium with their hydrates when dissolved in
aqueous solutions, as shown in the equation below:
Grignard reagents are required for a more permanent addition reaction of alkyl or aryl moiety to
a carbonyl group (Figure 6.30). Grignard reagents were first created by French chemist François
Auguste Victor Grignard, who was awarded the 1912 Nobel Prize in Chemistry for this work.
Addition of alky or aryl moiety to carbonyl groups is a very important reaction in organic
synthesis e.g. synthesis of drugs.
Figure 6.30 Addition of an alkyl moiety to carbonyl via the use of a Grignard reagent
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Question: What product forms when the Grignard reagent Ethyl-MgBr reacts with carbon
dioxide?
Substitution reactions
Substitution reactions occur when an atom or group of atoms is replaced by a different atom or
groups of atoms
Haloalkanes
Haloalkanes readily undergo substitution reactions with nucleophiles such as cyanide (Figure
6.31).
Figure 6.31 Substitution of Br with cyanide (CN− ion) to yield a nitrile
Substitution of haloalkanes is important in organic synthesis, in particular, the creation of
Grignard reagents as shown in the equation below:
Alcohol
Tertiary alcohols are usually more reactive the secondary and primary alcohols and would
readily undergo a substitution reaction with HCl to yield a chloroalkane (Figure 6.32).
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Figure 6.32 Substitution reaction of a tertiary alcohol
Low molecular weight primary and secondary alcohols would not react readily with HCl.
Substitution of primary and secondary alcohols require more reactive reagents such as thionyl
chloride (Figure 6.33).
Figure 6.33 Substitution reaction of a primary alcohol
Carbonyl
Esterification can be classified as a substitution reaction in which OH is replaced by an alcohol
(Figure 6.34). Substitution reactions of carbonyls usually involve the formation of a tetrahedral
intermediate. The leaving group would the detach resulting in a new substituted carbonyl
compound.
Figure 6.34 Esterification, a common substitution reaction. The tetrahedral intermediate is
shown in the middle and OH is the leaving group in this reaction.
A more general reaction can is shown in Figure 6.35. It should be noted that the leaving group
has to be a weaker base than the nucleophile. Otherwise the reaction will not happen.
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Figure 6.35 Generalized substitution reaction for carbonyl groups. Nucleophile and leaving
group highlighted in red and blue, respectively. Bottom equation show why the reaction cannot
proceed if the leaving group is not a weak base.
The chlorine in acid chlorides is a very weak base and thus acid chlorides can be substituted with
a wide variety of nucleophiles (Figure 6.36).
Figure 6.36 Substitution of acid chlorides
Elimination reactions
Elimination reactions occur when an atom or group of atoms is eliminated from a molecule
without replacement. This usually results in the formation of multiple bonds i.e. double or triple
bonds.
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Alkane
Alkanes can be undergo β-elimination in the presence of a very strong base such as sodium
ethoxide in ethanol. This reaction could yield multiple products. Zaitsev’s Rule states that
hydrogen is removed from the carbon with the fewest hydrogen atoms i.e. CH2 is more likely to
lose a H compared to CH3.
Figure 6.37 β-elimination of an alkane
Alcohols
Figure 6.38 Dehydration of alcohols
Alcohols can undergo dehydration (i.e. elimination of water) at high temperatures in the presence
of an acid catalyst (Figure 6.38). Notice the difference in reactivity between the two alcohols. In
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general, tertiary alcohols are more readily dehydrated followed by secondary alcohols and
primary alcohols.
Oxidation reactions
Oxidation reactions occur with the loss of electrons from an atom or molecule. In organic
chemistry this statement can be generalised as the addition of oxygen to a molecule
Alkene
Alkenes can easily be oxidized by potassium permanganate and other oxidizing agents. Type of
products formed depends on the reaction conditions. At cold temperatures with low
concentrations of oxidizing reagents, alkenes tend to form glycols (Figure 6.39).
Figure 6.39 Oxidation of an alkane by potassium
permanganate at ambient temperature
When more concentrated solutions of potassium permanganate and higher temperatures are
employed, the glycol is further oxidized. The molecule would be split into two, leading to the
formation of ketones or carboxylic acids depending on the subtituents of the alkene group
(Figure 6.40).
Figure 6.40 Oxidation of an alkane by potassium
permanganate at elevated temperatures
Alcohol
The hydroxyl group of alcohols can be oxidized into a carbonyl. Primary alcohols can be further
oxidized into carboxylic acid. For the production of vinegar, acetic acid bacteria is used as a
biological catalyst for the oxidation of ethanol (Figure 6.41).
Figure 6.41 Oxidation of ethanol, a primary alcohol
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Different reagents can be used to control the oxidation products of primary alcohols. Potassium
dichromate (K2Cr2O7), potassium permanganate (K2MnO4) and will oxidize primary alcohols
into carboxylic acids. Pyridinium chlorochromate (PCC) will only oxidize alcohols into
aldehydes or ketones.
PCC
K2MnO4
K2Cr2O7
K2MnO4
K2Cr2O7
PCC
Figure 6.42 Oxidation of primary and secondary alcohols
Question: Why is there no mention of tertiary alcohols?
Reduction reactions
Reduction reactions occur with the gain of electrons from an atom or molecule. In organic
chemistry this statement can be generalised as the addition of two hydrogen atoms to an
unsaturated hydrocarbon, aldehyde, ketone or carboxylic acid derivative.
Alkene
Alkene can be reduced by in the presence of a transition metal catalyst. Strictly speaking,
reduction of alkene is actually an addition reaction involving hydrogen. Compare Figure 6.43
with Figure 6.28.
Figure 6.43 Reduction of ethene to ethane
Figure 6.44 shows how the reaction is catalysed by a transition metal surface.
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Figure 6.44 Catalysis of hydrogenation
Carbonyl
Lithium aluminium hydride (LiAlH4) is a very strong reducing agent that is able to reduce
carbonyl into hydroxyl groups. Aldehydes are reduced to primary alcohols and ketone are
reduced to secondary alcohols (Figure 6.45).
Figure 6.45 Reduction of carbonyls by lithium aluminium hydride
Question: Ethyl pentanoate is used as a food additive to impart the flavour of apple. What would
be the two products from the reduction of ethyl pentanoate?
Reading Material

Chapters 15.1 to 15.4
Silberberg, M.S. (2006). Chemistry: The Molecular Nature of Matter and Change. 4th Ed.
McGraw Hill.
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